Showing 200 of total 457 results (show query)
bioc
xcms:LC-MS and GC-MS Data Analysis
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Maintained by Steffen Neumann. Last updated 2 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
124.1 match 196 stars 14.31 score 984 scripts 11 dependentsbioc
AlpsNMR:Automated spectraL Processing System for NMR
Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.
Maintained by Sergio Oller Moreno. Last updated 5 months ago.
softwarepreprocessingvisualizationclassificationcheminformaticsmetabolomicsdataimport
45.0 match 15 stars 7.59 score 12 scripts 1 dependentsbioc
ChIPseeker:ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
Maintained by Guangchuang Yu. Last updated 5 months ago.
annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics
25.2 match 234 stars 13.02 score 1.6k scripts 5 dependents
idslme
IDSL.IPA:Intrinsic Peak Analysis (IPA) for HRMS Data
A multi-layered untargeted pipeline for high-throughput LC/HRMS data processing to extract signals of organic small molecules. The package performs ion pairing, peak detection, peak table alignment, retention time correction, aligned peak table gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs). The 'IDSL.IPA' package was introduced in <doi:10.1021/acs.jproteome.2c00120> .
Maintained by Dinesh Barupal. Last updated 2 years ago.
exposomefeature-detectionlipidomicsmass-spectrometrymetabolomicspeak-detectionpeak-pickingsmall-moleculeuntargeted-metabolomics
62.2 match 13 stars 4.89 score 1 scripts 4 dependents
ethanbass
chromatographR:Chromatographic Data Analysis Toolset
Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in 'alsace' (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. <doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available using parametric time warping (as implemented in the 'ptw' package) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (as implemented in 'VPdtw') (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>). Peak-finding uses the algorithm by Tom O'Haver <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. <doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and suggested workflow.
Maintained by Ethan Bass. Last updated 8 days ago.
bioinformaticscheminformaticschromatographygc-fidhplchplc-dadhplc-pdahplv-uvmetabolomicsopen-dataopen-sciencereproducibilityreproducible-research
46.6 match 18 stars 6.33 score 8 scripts 1 dependentsbioc
EpiCompare:Comparison, Benchmarking & QC of Epigenomic Datasets
EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.
Maintained by Hiranyamaya Dash. Last updated 30 days ago.
epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsatacseqdnaseseqbenchmarkbenchmarkingbioconductorbioconductor-packagecomparisonhtmlinteractive-reporting
31.6 match 14 stars 7.54 score 46 scriptsbioc
GRaNIE:GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data
Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have cell-type specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using single-cell or bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally (Capture) Hi-C data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.
Maintained by Christian Arnold. Last updated 5 months ago.
softwaregeneexpressiongeneregulationnetworkinferencegenesetenrichmentbiomedicalinformaticsgeneticstranscriptomicsatacseqrnaseqgraphandnetworkregressiontranscriptionchipseq
41.8 match 5.40 score 24 scripts
wasquith
lmomco:L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments, and Many Distributions
Extensive functions for Lmoments (LMs) and probability-weighted moments (PWMs), distribution parameter estimation, LMs for distributions, LM ratio diagrams, multivariate Lcomoments, and asymmetric (asy) trimmed LMs (TLMs). Maximum likelihood and maximum product spacings estimation are available. Right-tail and left-tail LM censoring by threshold or indicator variable are available. LMs of residual (resid) and reversed (rev) residual life are implemented along with 13 quantile operators for reliability analyses. Exact analytical bootstrap estimates of order statistics, LMs, and LM var-covars are available. Harri-Coble Tau34-squared Normality Test is available. Distributions with L, TL, and added (+) support for right-tail censoring (RC) encompass: Asy Exponential (Exp) Power [L], Asy Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen) Exp Poisson [L], Gen Extreme Value [L], Gen Lambda [L, TL], Gen Logistic [L], Gen Normal [L], Gen Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L], Kumaraswamy [L], Laplace [L], Linear Mean Residual Quantile Function [L], Normal [L], 3p log-Normal [L], Pearson Type III [L], Polynomial Density-Quantile 3 and 4 [L], Rayleigh [L], Rev-Gumbel [L+RC], Rice [L], Singh Maddala [L], Slash [TL], 3p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L].
Maintained by William Asquith. Last updated 1 months ago.
flood-frequency-analysisl-momentsmle-estimationmps-estimationprobability-distributionrainfall-frequency-analysisreliability-analysisrisk-analysissurvival-analysis
26.0 match 2 stars 8.06 score 458 scripts 38 dependents
yufree
enviGCMS:GC/LC-MS Data Analysis for Environmental Science
Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Maintained by Miao YU. Last updated 2 months ago.
environmentmass-spectrometrymetabolomics
32.0 match 17 stars 6.49 score 30 scripts 1 dependentsbioc
Cardinal:A mass spectrometry imaging toolbox for statistical analysis
Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
Maintained by Kylie Ariel Bemis. Last updated 3 months ago.
softwareinfrastructureproteomicslipidomicsmassspectrometryimagingmassspectrometryimmunooncologynormalizationclusteringclassificationregression
19.0 match 47 stars 10.34 score 200 scriptsbioc
RMassBank:Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Maintained by RMassBank at Eawag. Last updated 5 months ago.
immunooncologybioinformaticsmassspectrometrymetabolomicssoftwareopenjdk
30.5 match 6.19 score 26 scriptsbioc
MassSpecWavelet:Peak Detection for Mass Spectrometry data using wavelet-based algorithms
Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See <doi:10.1093/bioinformatics/btl355} for further details.
Maintained by Sergio Oller Moreno. Last updated 3 months ago.
immunooncologymassspectrometryproteomicspeakdetection
19.8 match 9 stars 9.38 score 37 scripts 17 dependents
mottensmann
GCalignR:Simple Peak Alignment for Gas-Chromatography Data
Aligns peak based on peak retention times and matches homologous peaks across samples. The underlying alignment procedure comprises three sequential steps. (1) Full alignment of samples by linear transformation of retention times to maximise similarity among homologous peaks (2) Partial alignment of peaks within a user-defined retention time window to cluster homologous peaks (3) Merging rows that are likely representing homologous substances (i.e. no sample shows peaks in both rows and the rows have similar retention time means). The algorithm is described in detail in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
Maintained by Meinolf Ottensmann. Last updated 6 months ago.
28.2 match 5 stars 6.39 score 41 scripts
beirnaert
speaq:Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations
Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More details can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.
Maintained by Charlie Beirnaert. Last updated 3 years ago.
24.1 match 9 stars 7.02 score 26 scripts 3 dependents
stuart-lab
Signac:Analysis of Single-Cell Chromatin Data
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Maintained by Tim Stuart. Last updated 7 months ago.
atacbioinformaticssingle-cellzlibcpp
13.9 match 349 stars 12.19 score 3.7k scripts 1 dependentsbioc
seqsetvis:Set Based Visualizations for Next-Gen Sequencing Data
seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.
Maintained by Joseph R Boyd. Last updated 3 months ago.
softwarechipseqmultiplecomparisonsequencingvisualization
28.5 match 5.82 score 82 scriptsbioc
matter:Out-of-core statistical computing and signal processing
Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images.
Maintained by Kylie A. Bemis. Last updated 3 months ago.
infrastructuredatarepresentationdataimportdimensionreductionpreprocessingcpp
16.4 match 57 stars 9.52 score 64 scripts 2 dependentsbioc
chipenrich:Gene Set Enrichment For ChIP-seq Peak Data
ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.
Maintained by Kai Wang. Last updated 4 days ago.
immunooncologychipseqepigeneticsfunctionalgenomicsgenesetenrichmenthistonemodificationregression
30.3 match 4.94 score 29 scriptsbioc
rmspc:Multiple Sample Peak Calling
The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as "peaks"), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate samples are analyzed, overlapping peaks are expected. This repeated evidence can therefore be used to locally lower the minimum significance required to accept a peak. MSPC uses combined evidence from replicated experiments to evaluate peak calling output, rescuing peaks, and reduce false positives. It takes any number of replicates as input and improves sensitivity and specificity of peak calling on each, and identifies consensus regions between the input samples.
Maintained by Meriem Bahda. Last updated 19 days ago.
chipseqsequencingchiponchipdataimportrnaseqanalysischip-seqenriched-regionsgenome-analysismspcnext-generation-sequencingngs-analysisoverlapping-peakspeakpeaks
34.6 match 20 stars 4.08 score 5 scripts
peter-t-ruehr
forceR:Force Measurement Analyses
For cleaning and analysis of graphs, such as animal closing force measurements. 'forceR' was initially written and optimized to deal with insect bite force measurements, but can be used for any time series. Includes a full workflow to load, plot and crop data, correct amplifier and baseline drifts, identify individual peak shapes (bites), rescale (normalize) peak curves, and find best polynomial fits to describe and analyze force curve shapes.
Maintained by Peter T. Rühr. Last updated 12 months ago.
36.9 match 3.70 score 10 scriptsbioc
TargetSearch:A package for the analysis of GC-MS metabolite profiling data
This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.
Maintained by Alvaro Cuadros-Inostroza. Last updated 4 months ago.
massspectrometrypreprocessingdecisiontreeimmunooncologybiocbioconductorgc-msmass-spectrometry
18.4 match 4 stars 7.42 score 3 scriptsyufree
pmd:Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis
Paired mass distance (PMD) analysis proposed in Yu, Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062> and PMD based reactomics analysis proposed in Yu and Petrick (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid chromatography–mass spectrometry (GC/LC-MS) based non-targeted analysis. PMD analysis including GlobalStd algorithm and structure/reaction directed analysis. GlobalStd algorithm could found independent peaks in m/z-retention time profiles based on retention time hierarchical cluster analysis and frequency analysis of paired mass distances within retention time groups. Structure directed analysis could be used to find potential relationship among those independent peaks in different retention time groups based on frequency of paired mass distances. Reactomics analysis could also be performed to build PMD network, assign sources and make biomarker reaction discovery. GUIs for PMD analysis is also included as 'shiny' applications.
Maintained by Miao YU. Last updated 2 months ago.
mass-spectrometrymetabolomicsnon-target
20.4 match 10 stars 6.68 score 40 scriptsbioc
target:Predict Combined Function of Transcription Factors
Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) <doi: 10.1038/nprot.2013.150>. Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.
Maintained by Mahmoud Ahmed. Last updated 5 months ago.
softwarestatisticalmethodtranscriptionalgorithmchip-seqdna-bindinggene-regulationtranscription-factors
15.9 match 4 stars 7.79 score 1.3k scriptsbioc
Spectra:Spectra Infrastructure for Mass Spectrometry Data
The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 9 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductorhacktoberfestmass-spectrometry
9.4 match 41 stars 13.01 score 254 scripts 35 dependentsbioc
geneXtendeR:Optimized Functional Annotation Of ChIP-seq Data
geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.
Maintained by Bohdan Khomtchouk. Last updated 5 months ago.
chipseqgeneticsannotationgenomeannotationdifferentialpeakcallingcoveragepeakdetectionchiponchiphistonemodificationdataimportnaturallanguageprocessingvisualizationgosoftwarebioconductorbioinformaticscchip-seqcomputational-biologyepigeneticsfunctional-annotation
28.7 match 9 stars 3.95 score 5 scripts
adafede
cascade:Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts
This package provides the infrastructure to perform Automated Composition Assessment of Natural Extracts.
Maintained by Adriano Rutz. Last updated 11 days ago.
metabolite annotationcharged aerosol detectorsemi-quantitativenatural productscomputational metabolomicsspecialized metabolome
19.5 match 2 stars 5.74 score 40 scripts 1 dependents
sgibb
MALDIquant:Quantitative Analysis of Mass Spectrometry Data
A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Maintained by Sebastian Gibb. Last updated 7 months ago.
maldimaldi-imsmaldi-tof-msmass-spectrometry
10.1 match 62 stars 11.06 score 180 scripts 44 dependentsbioc
ChIPQC:Quality metrics for ChIPseq data
Quality metrics for ChIPseq data.
Maintained by Tom Carroll. Last updated 5 months ago.
sequencingchipseqqualitycontrolreportwriting
19.8 match 5.45 score 140 scripts
piplus2
SPUTNIK:Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit
Set of tools for peak filtering of mass spectrometry imaging data based on spatial distribution of signal. Given a region-of-interest, representing the spatial region where the informative signal is expected to be localized, a series of filters determine which peak signals are characterized by an implausible spatial distribution. The filters reduce the dataset dimension and increase its information vs noise ratio, improving the quality of the unsupervised analysis results, reducing data dimension and simplifying the chemical interpretation. The methods are described in Inglese P. et al (2019) <doi:10.1093/bioinformatics/bty622>.
Maintained by Paolo Inglese. Last updated 11 months ago.
bioinformaticsdesi-msiimage-processingmaldi-msimaldi-tof-msmass-spectrometrymass-spectrometry-imaging
20.1 match 4 stars 5.24 score 43 scripts
aphalo
photobiology:Photobiological Calculations
Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Maintained by Pedro J. Aphalo. Last updated 2 days ago.
lightphotobiologyquantificationr4photobiology-suiteradiationspectrasun-position
10.7 match 4 stars 9.35 score 604 scripts 12 dependents
cbielow
PTXQC:Quality Report Generation for MaxQuant and mzTab Results
Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
Maintained by Chris Bielow. Last updated 1 years ago.
drag-and-drophacktoberfestheatmapmatch-between-runsmaxquantmetricmztabopenmsproteomicsquality-controlquality-metricsreport
10.4 match 42 stars 9.35 score 105 scripts 1 dependentsbioc
ChromSCape:Analysis of single-cell epigenomics datasets with a Shiny App
ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.
Maintained by Pacome Prompsy. Last updated 5 months ago.
shinyappssoftwaresinglecellchipseqatacseqmethylseqclassificationclusteringepigeneticsprincipalcomponentannotationbatcheffectmultiplecomparisonnormalizationpathwayspreprocessingqualitycontrolreportwritingvisualizationgenesetenrichmentdifferentialpeakcallingepigenomicsshinysingle-cellcpp
16.4 match 14 stars 5.83 score 16 scriptsbioc
idr2d:Irreproducible Discovery Rate for Genomic Interactions Data
A tool to measure reproducibility between genomic experiments that produce two-dimensional peaks (interactions between peaks), such as ChIA-PET, HiChIP, and HiC. idr2d is an extension of the original idr package, which is intended for (one-dimensional) ChIP-seq peaks.
Maintained by Konstantin Krismer. Last updated 5 months ago.
dna3dstructuregeneregulationpeakdetectionepigeneticsfunctionalgenomicsclassificationhic
21.5 match 4.30 score 6 scriptsbioc
PROcess:Ciphergen SELDI-TOF Processing
A package for processing protein mass spectrometry data.
Maintained by Xiaochun Li. Last updated 5 months ago.
immunooncologymassspectrometryproteomics
15.3 match 6.04 score 552 scriptsbioc
adductomicsR:Processing of adductomic mass spectral datasets
Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.
Maintained by Josie Hayes. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarethirdpartyclientdataimportgui
22.6 match 1 stars 4.00 score 5 scripts
hwborchers
pracma:Practical Numerical Math Functions
Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.
Maintained by Hans W. Borchers. Last updated 1 years ago.
7.1 match 29 stars 12.34 score 6.6k scripts 931 dependents
cemos-mannheim
MALDIcellassay:Automated MALDI Cell Assays Using Dose-Response Curve Fitting
Conduct automated cell-based assays using Matrix-Assisted Laser Desorption/Ionization (MALDI) methods for high-throughput screening of signals responsive to treatments. The package efficiently identifies high variance signals and fits dose-response curves to them. Quality metrics such as Z', V', log2 Fold-Change, and Curve response score (CRS) are provided for evaluating the potential of signals as biomarkers. The methodologies were introduced by Weigt et al. (2018) <doi:10.1038/s41598-018-29677-z> and refined by Unger et al. (2021) <doi:10.1038/s41596-021-00624-z>.
Maintained by Thomas Enzlein. Last updated 2 months ago.
cell-based-assayconcentration-response-analysismaldi-tof-msmass-spectrometryuntargeted-metabolomics
18.5 match 4.74 score 9 scripts
shotaochi
scorepeak:Peak Functions for Peak Detection in Univariate Time Series
Provides peak functions, which enable us to detect peaks in time series. The methods implemented in this package are based on Girish Keshav Palshikar (2009) <https://www.researchgate.net/publication/228853276_Simple_Algorithms_for_Peak_Detection_in_Time-Series>.
Maintained by Shota Ochi. Last updated 4 years ago.
23.5 match 1 stars 3.70 score 6 scriptsbioc
chipseq:chipseq: A package for analyzing chipseq data
Tools for helping process short read data for chipseq experiments.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
chipseqsequencingcoveragequalitycontroldataimport
13.3 match 6.34 score 91 scripts 4 dependents
joshuaulrich
quantmod:Quantitative Financial Modelling Framework
Specify, build, trade, and analyse quantitative financial trading strategies.
Maintained by Joshua M. Ulrich. Last updated 14 days ago.
algorithmic-tradingchartingdata-importfinancetime-series
5.2 match 839 stars 16.17 score 8.1k scripts 343 dependents
japal
MALDIrppa:MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis
Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data (Palarea-Albaladejo et al. (2018) <doi:10.1093/bioinformatics/btx628>).
Maintained by Javier Palarea-Albaladejo. Last updated 1 years ago.
mass-spectrometrypre-processing
13.6 match 2 stars 6.06 score 32 scripts 1 dependents
moseleybioinformaticslab
ScanCentricPeakCharacterization:Functionality for Characterizing Peaks in Mass Spectrometry in a Scan-Centric Manner
Provides a functions and classes for detecting, characterizing, and integrating peaks in a scan-centric manner from direct-injection mass spectrometry data.
Maintained by Robert M Flight. Last updated 12 months ago.
27.1 match 3.00 score 1 scriptsbioc
MotifPeeker:Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.
Maintained by Hiranyamaya Dash. Last updated 2 months ago.
epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsmotifdiscoverysequencematchingsoftwarealignmentbioconductorbioconductor-packagechip-seqepigenomicsinteractive-reportmotif-enrichment-analysis
14.7 match 2 stars 5.48 score 6 scriptsbioc
gcapc:GC Aware Peak Caller
Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.
Maintained by Mingxiang Teng. Last updated 5 months ago.
sequencingchipseqbatcheffectpeakdetection
15.9 match 9 stars 4.95 score 7 scriptsbioc
peakPantheR:Peak Picking and Annotation of High Resolution Experiments
An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.
Maintained by Arnaud Wolfer. Last updated 5 months ago.
massspectrometrymetabolomicspeakdetectionfeature-detectionmass-spectrometry
11.5 match 12 stars 6.82 score 23 scripts
noemiallefs
andurinha:Make Spectroscopic Data Processing Easier
The goal of 'andurinha' is provide a fast and friendly way to process spectroscopic data. It is intended for processing several spectra of samples with similar composition (tens to hundreds of spectra). It compiles spectroscopy data files, produces standardized and second derivative spectra, finds peaks and allows to select the most significant ones based on the second derivative/absorbance sum spectrum. It also provides functions for graphic evaluation of the outputs.
Maintained by Noemi Alvarez Fernandez. Last updated 2 years ago.
peakspeaks-selectionspectroscopy
21.0 match 1 stars 3.70 score 6 scripts
rickhelmus
patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis
Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.
Maintained by Rick Helmus. Last updated 10 days ago.
mass-spectrometrynon-targetcppopenjdk
12.5 match 65 stars 6.22 score 43 scriptsbioc
ProtGenerics:Generic infrastructure for Bioconductor mass spectrometry packages
S4 generic functions and classes needed by Bioconductor proteomics packages.
Maintained by Laurent Gatto. Last updated 2 months ago.
infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics
7.8 match 8 stars 9.43 score 4 scripts 188 dependents
r-forge
POT:Generalized Pareto Distribution and Peaks Over Threshold
Some functions useful to perform a Peak Over Threshold analysis in univariate and bivariate cases, see Beirlant et al. (2004) <doi:10.1002/0470012382>. A user guide is available in the vignette.
Maintained by Christophe Dutang. Last updated 5 months ago.
11.7 match 6.20 score 105 scripts 2 dependentsbioc
MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Maintained by Laurent Gatto. Last updated 2 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
5.5 match 130 stars 12.81 score 772 scripts 36 dependentsbioc
esATAC:An Easy-to-use Systematic pipeline for ATACseq data analysis
This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.
Maintained by Zheng Wei. Last updated 5 months ago.
immunooncologysequencingdnaseqqualitycontrolalignmentpreprocessingcoverageatacseqdnaseseqatac-seqbioconductorpipelinecppopenjdk
11.4 match 23 stars 6.11 score 3 scripts
mooresm
serrsBayes:Bayesian Modelling of Raman Spectroscopy
Sequential Monte Carlo (SMC) algorithms for fitting a generalised additive mixed model (GAMM) to surface-enhanced resonance Raman spectroscopy (SERRS), using the method of Moores et al. (2016) <arXiv:1604.07299>. Multivariate observations of SERRS are highly collinear and lend themselves to a reduced-rank representation. The GAMM separates the SERRS signal into three components: a sequence of Lorentzian, Gaussian, or pseudo-Voigt peaks; a smoothly-varying baseline; and additive white noise. The parameters of each component of the model are estimated iteratively using SMC. The posterior distributions of the parameters given the observed spectra are represented as a population of weighted particles.
Maintained by Matt Moores. Last updated 4 years ago.
bayesianchemometricsramansequential-monte-carlospectroscopycpp
12.5 match 8 stars 5.46 score 36 scripts
rchlumsk
RavenR:Raven Hydrological Modelling Framework R Support and Analysis
Utilities for processing input and output files associated with the Raven Hydrological Modelling Framework. Includes various plotting functions, model diagnostics, reading output files into extensible time series format, and support for writing Raven input files. The 'RavenR' package is also archived at Chlumsky et al. (2020) <doi:10.5281/zenodo.4248183>. The Raven Hydrologic Modelling Framework method can be referenced with Craig et al. (2020) <doi:10.1016/j.envsoft.2020.104728>.
Maintained by Robert Chlumsky. Last updated 4 months ago.
diagnosticshydrologymodelingmodellingvisualizationwaterwater-resourceswatershedcpp
9.6 match 36 stars 7.06 score 20 scripts
kbroman
qtl:Tools for Analyzing QTL Experiments
Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Maintained by Karl W Broman. Last updated 7 months ago.
5.3 match 80 stars 12.79 score 2.4k scripts 29 dependentsbioc
epigraHMM:Epigenomic R-based analysis with hidden Markov models
epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.
Maintained by Pedro Baldoni. Last updated 5 months ago.
chipseqatacseqdnaseseqhiddenmarkovmodelepigeneticszlibopenblascppopenmp
13.5 match 4.94 score 88 scripts
statist7
sitar:Super Imposition by Translation and Rotation Growth Curve Analysis
Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales. The model was first described by Lindstrom (1995) <doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole et al (2010) <doi:10.1093/ije/dyq115>.
Maintained by Tim Cole. Last updated 2 months ago.
7.4 match 13 stars 8.69 score 58 scripts 3 dependents
tdhock
PeakSegJoint:Joint Peak Detection in Several ChIP-Seq Samples
Jointly segment several ChIP-seq samples to find the peaks which are the same and different across samples. The fast approximate maximum Poisson likelihood algorithm is described in "PeakSegJoint: fast supervised peak detection via joint segmentation of multiple count data samples" <doi:10.48550/arXiv.1506.01286> by TD Hocking and G Bourque.
Maintained by Toby Dylan Hocking. Last updated 3 months ago.
15.6 match 5 stars 4.00 score 66 scripts
zachariahmclean
trace:Tandem Repeat Analysis by Capillary Electrophoresis
A pipeline for short tandem repeat instability analysis from fragment analysis data. Inputs of fsa files or peak tables, and a user supplied metadata data-frame. The package identifies ladders, calls peaks, identifies the modal peaks, calls repeats, then calculates repeat instability metrics (e.g. expansion index from Lee et al. (2010) <doi:10.1186/1752-0509-4-29>).
Maintained by Zachariah McLean. Last updated 2 days ago.
10.7 match 1 stars 5.61 score 74 scriptsbioc
IPO:Automated Optimization of XCMS Data Processing parameters
The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.
Maintained by Thomas Lieb. Last updated 5 months ago.
immunooncologymetabolomicsmassspectrometry
7.2 match 34 stars 8.14 score 41 scripts
braverock
PerformanceAnalytics:Econometric Tools for Performance and Risk Analysis
Collection of econometric functions for performance and risk analysis. In addition to standard risk and performance metrics, this package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.
Maintained by Brian G. Peterson. Last updated 3 months ago.
3.7 match 222 stars 15.93 score 4.8k scripts 20 dependentsbioc
extraChIPs:Additional functions for working with ChIP-Seq data
This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.
Maintained by Stevie Pederson. Last updated 15 days ago.
8.8 match 7 stars 6.67 score 25 scripts
bnprks
BPCells:Single Cell Counts Matrices to PCA
> Efficient operations for single cell ATAC-seq fragments and RNA counts matrices. Interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.
Maintained by Benjamin Parks. Last updated 1 months ago.
7.7 match 184 stars 7.48 score 172 scriptsbioc
SIMAT:GC-SIM-MS data processing and alaysis tool
This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.
Maintained by M. R. Nezami Ranjbar. Last updated 5 months ago.
immunooncologysoftwaremetabolomicsmassspectrometry
13.5 match 4.26 score 1 scriptsbioc
msPurity:Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.
Maintained by Thomas N. Lawson. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarebioconductor-packagedimsfragmentationlc-mslc-msmsmass-spectrometryprecursor-ion-purity
8.1 match 15 stars 7.03 score 44 scripts
jdtuck
fdasrvf:Elastic Functional Data Analysis
Performs alignment, PCA, and modeling of multidimensional and unidimensional functions using the square-root velocity framework (Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic analysis of functional data through phase and amplitude separation.
Maintained by J. Derek Tucker. Last updated 27 days ago.
7.3 match 11 stars 7.74 score 83 scripts 3 dependentsbioc
Damsel:Damsel: an end to end analysis of DamID
Damsel provides an end to end analysis of DamID data. Damsel takes bam files from Dam-only control and fusion samples and counts the reads matching to each GATC region. edgeR is utilised to identify regions of enrichment in the fusion relative to the control. Enriched regions are combined into peaks, and are associated with nearby genes. Damsel allows for IGV style plots to be built as the results build, inspired by ggcoverage, and using the functionality and layering ability of ggplot2. Damsel also conducts gene ontology testing with bias correction through goseq, and future versions of Damsel will also incorporate motif enrichment analysis. Overall, Damsel is the first package allowing for an end to end analysis with visual capabilities. The goal of Damsel was to bring all the analysis into one place, and allow for exploratory analysis within R.
Maintained by Caitlin Page. Last updated 5 months ago.
differentialmethylationpeakdetectiongenepredictiongenesetenrichment
10.5 match 5.34 score 20 scripts
oskarhansson
strvalidator:Process Control and Validation of Forensic STR Kits
An open source platform for validation and process control. Tools to analyze data from internal validation of forensic short tandem repeat (STR) kits are provided. The tools are developed to provide the necessary data to conform with guidelines for internal validation issued by the European Network of Forensic Science Institutes (ENFSI) DNA Working Group, and the Scientific Working Group on DNA Analysis Methods (SWGDAM). A front-end graphical user interface is provided. More information about each function can be found in the respective help documentation.
Maintained by Oskar Hansson. Last updated 2 months ago.
13.0 match 5 stars 4.29 score 13 scriptsbioc
memes:motif matching, comparison, and de novo discovery using the MEME Suite
A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows.
Maintained by Spencer Nystrom. Last updated 5 months ago.
dataimportfunctionalgenomicsgeneregulationmotifannotationmotifdiscoverysequencematchingsoftware
6.3 match 49 stars 8.68 score 117 scripts 1 dependents
crp2a
gamma:Dose Rate Estimation from in-Situ Gamma-Ray Spectrometry Measurements
Process in-situ Gamma-Ray Spectrometry for Luminescence Dating. This package allows to import, inspect and correct the energy shifts of gamma-ray spectra. It provides methods for estimating the gamma dose rate by the use of a calibration curve as described in Mercier and Falguères (2007). The package only supports Canberra CNF and TKA and Kromek SPE files.
Maintained by Archéosciences Bordeaux. Last updated 6 months ago.
archaeometrygamma-spectrometrygeochronologyluminescence-dating
7.8 match 6 stars 6.99 score 11 scripts 1 dependentsbioc
CAMERA:Collection of annotation related methods for mass spectrometry data
Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments
Maintained by Steffen Neumann. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
5.3 match 11 stars 10.27 score 175 scripts 6 dependentsaphalo
ggpmisc:Miscellaneous Extensions to 'ggplot2'
Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Statistics: locate and tag peaks and valleys; label plot with the equation of a fitted polynomial or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' and 'broom.mixed' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.
Maintained by Pedro J. Aphalo. Last updated 4 months ago.
data-analysisdatavizggplot2-annotationsggplot2-statsstatistics
4.1 match 105 stars 13.32 score 4.4k scripts 14 dependentsbioc
ptairMS:Pre-processing PTR-TOF-MS Data
This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a singl<e ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation and feature annotation. Applications to exhaled air and cell culture in headspace are described in the vignettes and examples. This package was used for data analysis of Gassin Delyle study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS), and permit to identfy four potentiel biomarquers of the infection.
Maintained by camille Roquencourt. Last updated 5 months ago.
softwaremassspectrometrypreprocessingmetabolomicspeakdetectionalignmentcpp
10.5 match 7 stars 5.15 score 3 scriptsbioc
NADfinder:Call wide peaks for sequencing data
Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation.
Maintained by Jianhong Ou. Last updated 2 months ago.
sequencingdnaseqgeneregulationpeakdetection
12.8 match 4.18 score 1 scriptsbioc
DiffBind:Differential Binding Analysis of ChIP-Seq Peak Data
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
Maintained by Rory Stark. Last updated 2 months ago.
sequencingchipseqatacseqdnaseseqmethylseqripseqdifferentialpeakcallingdifferentialmethylationgeneregulationhistonemodificationpeakdetectionbiomedicalinformaticscellbiologymultiplecomparisonnormalizationreportwritingepigeneticsfunctionalgenomicscurlbzip2xz-utilszlibcpp
7.4 match 7.13 score 512 scripts 2 dependents
rqtl
qtl2:Quantitative Trait Locus Mapping in Experimental Crosses
Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Maintained by Karl W Broman. Last updated 8 days ago.
5.4 match 34 stars 9.48 score 1.1k scripts 5 dependentsbioc
mspms:Tools for the analysis of MSP-MS data
This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.
Maintained by Charlie Bayne. Last updated 3 months ago.
proteomicsmassspectrometrypreprocessingproteaseproteomics-data-analysis
10.3 match 4.95 score 4 scripts
tpq
peakRAM:Monitor the Total and Peak RAM Used by an Expression or Function
When working with big data sets, RAM conservation is critically important. However, it is not always enough to just monitor the size of the objects created. So-called "copy-on-modify" behavior, characteristic of R, means that some expressions or functions may require an unexpectedly large amount of RAM overhead. For example, replacing a single value in a matrix duplicates that matrix in the back-end, making this task require twice as much RAM as that used by the matrix itself. This package makes it easy to monitor the total and peak RAM used so that developers can quickly identify and eliminate RAM hungry code.
Maintained by Thomas Quinn. Last updated 4 years ago.
8.2 match 20 stars 6.14 score 139 scripts
matthiaspucher
staRdom:PARAFAC Analysis of EEMs from DOM
'This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.'
Maintained by Matthias Pucher. Last updated 4 months ago.
8.2 match 21 stars 6.03 score 86 scripts
pmassicotte
eemR:Tools for Pre-Processing Emission-Excitation-Matrix (EEM) Fluorescence Data
Provides various tools for preprocessing Emission-Excitation-Matrix (EEM) for Parallel Factor Analysis (PARAFAC). Different methods are also provided to calculate common metrics such as humification index and fluorescence index.
Maintained by Philippe Massicotte. Last updated 3 years ago.
dissolved-organic-matteremissionexcitationfluorescenceoptics
7.2 match 19 stars 6.87 score 65 scripts 1 dependents
nanxstats
oneclust:Maximum Homogeneity Clustering for Univariate Data
Maximum homogeneity clustering algorithm for one-dimensional data described in W. D. Fisher (1958) <doi:10.1080/01621459.1958.10501479> via dynamic programming.
Maintained by Nan Xiao. Last updated 1 years ago.
clustering-algorithmfeature-engineeringhomogeneitypeak-callingunivariate-datacpp
11.2 match 5 stars 4.40 score
paulnorthrop
threshr:Threshold Selection and Uncertainty for Extreme Value Analysis
Provides functions for the selection of thresholds for use in extreme value models, based mainly on the methodology in Northrop, Attalides and Jonathan (2017) <doi:10.1111/rssc.12159>. It also performs predictive inferences about future extreme values, based either on a single threshold or on a weighted average of inferences from multiple thresholds, using the 'revdbayes' package <https://cran.r-project.org/package=revdbayes>. At the moment only the case where the data can be treated as independent identically distributed observations is considered.
Maintained by Paul J. Northrop. Last updated 1 months ago.
extreme-value-statisticsextremesgeneralizedinferenceparetoplotpredictionthresholdthreshold-selectionuncertainty
8.6 match 6 stars 5.72 score 29 scripts 1 dependentsbioc
FindIT2:find influential TF and Target based on multi-omics data
This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.
Maintained by Guandong Shang. Last updated 5 months ago.
softwareannotationchipseqatacseqgeneregulationmultiplecomparisongenetarget
9.3 match 6 stars 5.26 score 7 scripts
reconverse
i2extras:Functions to Work with 'incidence2' Objects
Provides functions to work with 'incidence2' objects, including a simplified interface for trend fitting and peak estimation. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis (<https://www.reconverse.org/).
Maintained by Tim Taylor. Last updated 7 months ago.
9.2 match 2 stars 5.25 score 22 scripts
lmrodriguezr
enveomics.R:Various Utilities for Microbial Genomics and Metagenomics
A collection of functions for microbial ecology and other applications of genomics and metagenomics. Companion package for the Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016 <DOI:10.7287/peerj.preprints.1900v1>).
Maintained by Luis M. Rodriguez-R. Last updated 1 months ago.
21.8 match 2.17 score 26 scriptsbioc
doubletrouble:Identification and classification of duplicated genes
doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.
Maintained by Fabrício Almeida-Silva. Last updated 3 days ago.
softwarewholegenomecomparativegenomicsfunctionalgenomicsphylogeneticsnetworkclassificationbioinformaticscomparative-genomicsgene-duplicationmolecular-evolutionwhole-genome-duplication
7.3 match 23 stars 6.44 score 17 scriptsbioc
COCOA:Coordinate Covariation Analysis
COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.
Maintained by John Lawson. Last updated 5 months ago.
epigeneticsdnamethylationatacseqdnaseseqmethylseqmethylationarrayprincipalcomponentgenomicvariationgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqsequencingimmunooncologydna-methylationpca
6.6 match 10 stars 7.02 score 21 scripts
chr1swallace
coloc:Colocalisation Tests of Two Genetic Traits
Performs the colocalisation tests described in Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>, Wallace (2020) <doi:10.1371/journal.pgen.1008720>, Wallace (2021) <doi:10.1371/journal.pgen.1009440>.
Maintained by Chris Wallace. Last updated 4 months ago.
3.7 match 162 stars 12.23 score 916 scripts 3 dependents
doi-usgs
dataRetrieval:Retrieval Functions for USGS and EPA Hydrology and Water Quality Data
Collection of functions to help retrieve U.S. Geological Survey and U.S. Environmental Protection Agency water quality and hydrology data from web services. Data are discovered from National Water Information System <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>. Water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Maintained by Laura DeCicco. Last updated 17 days ago.
3.1 match 280 stars 14.18 score 1.7k scripts 15 dependentsbioc
epiregulon:Gene regulatory network inference from single cell epigenomic data
Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.
Maintained by Xiaosai Yao. Last updated 6 days ago.
singlecellgeneregulationnetworkinferencenetworkgeneexpressiontranscriptiongenetargetcpp
6.7 match 14 stars 6.67 score 17 scripts
bioxgeo
geodiv:Methods for Calculating Gradient Surface Metrics
Methods for calculating gradient surface metrics for continuous analysis of landscape features.
Maintained by Annie C. Smith. Last updated 1 years ago.
7.5 match 11 stars 5.88 score 23 scripts 1 dependents
cran
wearables:Tools to Read and Convert Wearables Data
Package to read Empatica E4 data, perform several transformations, perform signal processing and analyses, including batch analyses.
Maintained by Peter de Looff. Last updated 3 years ago.
23.1 match 1 stars 1.90 score 16 scripts
aahani-r
FloodFreqPlot:Flood Probability Plotting and Graphical Frequency Analysis
Plotting flood quantiles and their corresponding probabilities (return periods) on the probability papers. The details of relevant methods are available in Chow et al (1988, ISBN: 007070242X, 9780070702424), and Bobee and Ashkar (1991, ISBN: 0918334683, 9780918334688).
Maintained by Ali Ahani. Last updated 3 years ago.
25.7 match 1.70 scorebioc
MMDiff2:Statistical Testing for ChIP-Seq data sets
This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).
Maintained by Gabriele Schweikert. Last updated 5 months ago.
chipseqdifferentialpeakcallingsequencingsoftware
13.0 match 3.30 score
eonurk
cinaR:A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data analyses. This package combines different packages to have an ultimate package for both data analyses and visualization of 'ATAC-seq' data. Methods are described in 'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.
Maintained by Onur Karakaslar. Last updated 10 months ago.
atac-seqdifferential-analysisenrichment-analysisgene-sets
7.8 match 13 stars 5.52 score 51 scripts
qianli10000
GMSimpute:Generalized Mass Spectrum Missing Peaks Abundance Imputation
GMSimpute implements the Two-Step Lasso (TS-Lasso) and compound minimum to recover the abundance of missing peaks in mass spectrum analysis. TS-Lasso is a label-free imputation method that handles various types of missing peaks simultaneously. This package provides the procedure to generate missing peaks (or data) for simulation study, as well as a tool to estimate and visualize the proportion of missing at random.
Maintained by Qian Li. Last updated 6 years ago.
13.9 match 3.06 score 23 scriptsaphalo
ggspectra:Extensions to 'ggplot2' for Radiation Spectra
Additional annotations, stats, geoms and scales for plotting "light" spectra with 'ggplot2', together with specializations of ggplot() and autoplot() methods for spectral data and waveband definitions stored in objects of classes defined in package 'photobiology'. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Maintained by Pedro J. Aphalo. Last updated 2 days ago.
datavizggplot2-autoplotggplot2-enhancementesggplot2-geomsggplot2-scalesggplot2-statslightr4photobiology-suiteradiationspectra
5.3 match 5 stars 8.09 score 390 scripts 1 dependents
reconhub
incidence:Compute, Handle, Plot and Model Incidence of Dated Events
Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Maintained by Tim Taylor. Last updated 7 months ago.
3.5 match 58 stars 12.06 score 504 scripts 11 dependentsbioc
MAIT:Statistical Analysis of Metabolomic Data
The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.
Maintained by Pol Sola-Santos. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomicssoftware
9.2 match 4.60 score 20 scriptsbioc
MsCoreUtils:Core Utils for Mass Spectrometry Data
MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.
Maintained by RforMassSpectrometry Package Maintainer. Last updated 4 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometryutils
4.0 match 16 stars 10.52 score 41 scripts 71 dependentsbioc
motifTestR:Perform key tests for binding motifs in sequence data
Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results.
Maintained by Stevie Pederson. Last updated 8 days ago.
motifannotationchipseqchiponchipsequencematchingsoftware
8.5 match 1 stars 4.90 score 2 scriptsbioc
mosaics:MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.
Maintained by Dongjun Chung. Last updated 5 months ago.
chipseqsequencingtranscriptiongeneticsbioinformaticscpp
12.4 match 3.30 score 8 scripts
ltrr-arizona-edu
burnr:Forest Fire History Analysis
Tools to read, write, parse, and analyze forest fire history data (e.g. FHX). Described in Malevich et al. (2018) <doi:10.1016/j.dendro.2018.02.005>.
Maintained by Steven Malevich. Last updated 3 years ago.
citationdendrochronologyecologyforestfireplotscientificstatistics
6.9 match 15 stars 5.95 score 59 scripts
bhklab
CREAM:Clustering of Genomic Regions Analysis Method
Provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach.
Maintained by Benjamin Haibe-Kains. Last updated 4 years ago.
peakdetectionfunctionalpredictionbiomedicalinformaticsclusteringbiomedical-informaticsfunctional-predictionpeak-detection
7.5 match 12 stars 5.43 score 15 scripts
sujit-sahu
bmstdr:Bayesian Modeling of Spatio-Temporal Data with R
Fits, validates and compares a number of Bayesian models for spatial and space time point referenced and areal unit data. Model fitting is done using several packages: 'rstan', 'INLA', 'spBayes', 'spTimer', 'spTDyn', 'CARBayes' and 'CARBayesST'. Model comparison is performed using the DIC and WAIC, and K-fold cross-validation where the user is free to select their own subset of data rows for validation. Sahu (2022) <doi:10.1201/9780429318443> describes the methods in detail.
Maintained by Sujit K. Sahu. Last updated 1 years ago.
bayesianmodellingspatio-temporal-datacpp
8.0 match 15 stars 4.95 score 12 scriptscran
gcxgclab:GCxGC Preprocessing and Analysis
Provides complete detailed preprocessing of two-dimensional gas chromatogram (GCxGC) samples. Baseline correction, smoothing, peak detection, and peak alignment. Also provided are some analysis functions, such as finding extracted ion chromatograms, finding mass spectral data, targeted analysis, and nontargeted analysis with either the 'National Institute of Standards and Technology Mass Spectral Library' or with the mass data. There are also several visualization methods provided for each step of the preprocessing and analysis.
Maintained by Stephanie Gamble. Last updated 1 years ago.
19.3 match 2.00 score 1 scriptsbioc
mzR:parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
Maintained by Steffen Neumann. Last updated 1 months ago.
immunooncologyinfrastructuredataimportproteomicsmetabolomicsmassspectrometryzlibcpp
3.0 match 45 stars 12.77 score 204 scripts 44 dependents
welch-lab
rliger:Linked Inference of Genomic Experimental Relationships
Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
Maintained by Yichen Wang. Last updated 2 months ago.
nonnegative-matrix-factorizationsingle-cellopenblascpp
3.5 match 402 stars 10.80 score 334 scripts 1 dependents
kurthornik
mlbench:Machine Learning Benchmark Problems
A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.
Maintained by Kurt Hornik. Last updated 3 months ago.
4.3 match 2 stars 8.93 score 5.0k scripts 55 dependentsbioc
flagme:Analysis of Metabolomics GC/MS Data
Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.
Maintained by Mark Robinson. Last updated 5 months ago.
differentialexpressionmassspectrometry
8.8 match 4.30 score 2 scriptsreconverse
incidence2:Compute, Handle and Plot Incidence of Dated Events
Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence2' is used to store computed incidence and can be easily manipulated, subsetted, and plotted.
Maintained by Tim Taylor. Last updated 5 days ago.
4.9 match 17 stars 7.67 score 104 scripts 1 dependentsbioc
PeacoQC:Peak-based selection of high quality cytometry data
This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.
Maintained by Annelies Emmaneel. Last updated 5 months ago.
flowcytometryqualitycontrolpreprocessingpeakdetection
5.1 match 16 stars 7.38 score 28 scripts 3 dependentsbioc
pmp:Peak Matrix Processing and signal batch correction for metabolomics datasets
Methods and tools for (pre-)processing of metabolomics datasets (i.e. peak matrices), including filtering, normalisation, missing value imputation, scaling, and signal drift and batch effect correction methods. Filtering methods are based on: the fraction of missing values (across samples or features); Relative Standard Deviation (RSD) calculated from the Quality Control (QC) samples; the blank samples. Normalisation methods include Probabilistic Quotient Normalisation (PQN) and normalisation to total signal intensity. A unified user interface for several commonly used missing value imputation algorithms is also provided. Supported methods are: k-nearest neighbours (knn), random forests (rf), Bayesian PCA missing value estimator (bpca), mean or median value of the given feature and a constant small value. The generalised logarithm (glog) transformation algorithm is available to stabilise the variance across low and high intensity mass spectral features. Finally, this package provides an implementation of the Quality Control-Robust Spline Correction (QCRSC) algorithm for signal drift and batch effect correction of mass spectrometry-based datasets.
Maintained by Gavin Rhys Lloyd. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarequalitycontrolbatcheffect
8.1 match 4.60 score 33 scripts
muschellij2
WhiteStripe:White Matter Normalization for Magnetic Resonance Images
Shinohara (2014) <doi:10.1016/j.nicl.2014.08.008> introduced 'WhiteStripe', an intensity-based normalization of T1 and T2 images, where normal appearing white matter performs well, but requires segmentation. This method performs white matter mean and standard deviation estimates on data that has been rigidly-registered to the 'MNI' template and uses histogram-based methods.
Maintained by John Muschelli. Last updated 10 months ago.
6.0 match 9 stars 6.22 score 61 scripts
riazakhan94
loadshaper:Producing Load Shape with Target Peak and Load Factor
Modifying a load shape to match specific peak and load factor is a fundamental component for various power system planning and operation studies. This package is an efficient tool to modify a reference load shape while matching the desired peak and load factor. The package offers both linear and non-linear method, described in <https://rpubs.com/riazakhan94/load_shape_match_peak_energy>. The user can control the shape of the final load shape by regulating certain parameters. The package provides validation metrics for assessing the derived load shape in terms of preserving time series properties. It also offers powerful graphics, that allows the user to visually assess the derived load shape.
Maintained by Md Riaz Ahmed Khan. Last updated 3 years ago.
9.9 match 3.70 score 2 scriptsbioc
cfDNAPro:cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA
cfDNA fragments carry important features for building cancer sample classification ML models, such as fragment size, and fragment end motif etc. Analyzing and visualizing fragment size metrics, as well as other biological features in a curated, standardized, scalable, well-documented, and reproducible way might be time intensive. This package intends to resolve these problems and simplify the process. It offers two sets of functions for cfDNA feature characterization and visualization.
Maintained by Haichao Wang. Last updated 5 months ago.
visualizationsequencingwholegenomebioinformaticscancer-genomicscancer-researchcell-free-dnaearly-detectiongenomics-visualizationliquid-biopsyswgswhole-genome-sequencing
6.0 match 28 stars 6.04 score 13 scriptsbioc
chromVAR:Chromatin Variation Across Regions
Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.
Maintained by Alicia Schep. Last updated 5 months ago.
singlecellsequencinggeneregulationimmunooncologycpp
4.9 match 7.31 score 772 scriptsethanbass
mzinspectr:Read and Analyze Mass Spectrometry Alignment Files
A few functions for analyzing MS-DIAL alignments in R. Includes functions for feature normalization, subtraction of blanks, and mass library (msp) search.
Maintained by Ethan Bass. Last updated 5 months ago.
cheminformaticsgc-mslc-msmetabolomics
13.0 match 3 stars 2.78 score
jeromeecoac
seewave:Sound Analysis and Synthesis
Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses. See Sueur et al. (2008) <doi:10.1080/09524622.2008.9753600> and Sueur (2018) <doi:10.1007/978-3-319-77647-7>.
Maintained by Jerome Sueur. Last updated 1 years ago.
3.8 match 18 stars 8.88 score 880 scripts 23 dependents
rivasiker
ggHoriPlot:Horizon Plots for 'ggplot2'
A user-friendly, highly customizable R package for building horizon plots in the 'ggplot2' environment.
Maintained by Iker Rivas-González. Last updated 8 months ago.
data-sciencedata-visualizationggplot2horizon-plots
4.8 match 144 stars 6.96 score 63 scripts
lbelzile
evt0:Mean of Order P, Peaks over Random Threshold Hill and High Quantile Estimates
The R package proposes extreme value index estimators for heavy tailed models by mean of order p <DOI:10.1016/j.csda.2012.07.019>, peaks over random threshold <DOI:10.57805/revstat.v4i3.37> and a bias-reduced estimator <DOI:10.1080/00949655.2010.547196>. The package also computes moment, generalised Hill <DOI:10.2307/3318416> and mixed moment estimates for the extreme value index. High quantiles and value at risk estimators based on these estimators are implemented.
Maintained by Leo Belzile. Last updated 1 years ago.
11.9 match 2.81 score 13 scripts
bioc
GUIDEseq:GUIDE-seq and PEtag-seq analysis pipeline
The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.
Maintained by Lihua Julie Zhu. Last updated 5 months ago.
immunooncologygeneregulationsequencingworkflowstepcrispr
7.5 match 4.45 score 14 scripts
isoverse
isoorbi:Process Orbitrap Isotopocule Data
Read and process isotopocule data from an Orbitrap Isotope Solutions mass spectrometer. Citation: Kantnerova et al. (Nature Protocols, 2024).
Maintained by Caj Neubauer. Last updated 7 months ago.
5.2 match 4 stars 6.31 score 17 scripts
janlisec
CorrectOverloadedPeaks:Correct Overloaded Peaks from GC-APCI-MS Data
Analyzes and modifies metabolomics raw data (generated using Gas Chromatography-Atmospheric Pressure Chemical Ionization-Mass Spectrometry) to correct overloaded signals, i.e. ion intensities exceeding detector saturation leading to a cut-off peak. Data in 'xcmsRaw' format are accepted as input and 'mzXML' files can be processed alternatively. Overloaded signals are detected automatically and modified using an Gaussian or an Isotopic-Ratio approach. Quality control plots are generated and corrected data are stored within the original 'xcmsRaw' or 'mzXML' respectively to allow further processing.
Maintained by Jan Lisec. Last updated 17 days ago.
10.3 match 3.18 score 5 scripts 1 dependentsbioc
ncGTW:Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
The purpose of ncGTW is to help XCMS for LC-MS data alignment. Currently, ncGTW can detect the misaligned feature groups by XCMS, and the user can choose to realign these feature groups by ncGTW or not.
Maintained by Chiung-Ting Wu. Last updated 5 months ago.
softwaremassspectrometrymetabolomicsalignmentcpp
6.6 match 8 stars 4.90 score 3 scriptscran
astrochron:A Computational Tool for Astrochronology
Routines for astrochronologic testing, astronomical time scale construction, and time series analysis <doi:10.1016/j.earscirev.2018.11.015>. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.
Maintained by Stephen Meyers. Last updated 6 months ago.
8.4 match 5 stars 3.85 score 141 scripts
alanarnholt
BSDA:Basic Statistics and Data Analysis
Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.
Maintained by Alan T. Arnholt. Last updated 2 years ago.
3.4 match 7 stars 9.11 score 1.3k scripts 6 dependents
animint
animint2:Animated Interactive Grammar of Graphics
Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Maintained by Toby Hocking. Last updated 27 days ago.
3.5 match 64 stars 8.87 score 173 scriptstdhock
PeakError:Compute the Label Error of Peak Calls
Chromatin immunoprecipitation DNA sequencing results in genomic tracks that show enriched regions or peaks where proteins are bound. This package implements fast C code that computes the true and false positives with respect to a database of annotated region labels.
Maintained by Toby Dylan Hocking. Last updated 2 years ago.
9.5 match 4 stars 3.26 score 15 scripts 1 dependentscran
YEAB:Analyze Data from Analysis of Behavior Experiments
Analyze data from behavioral experiments conducted using 'MED-PC' software developed by Med Associates Inc. Includes functions to fit exponential and hyperbolic models for delay discounting tasks, exponential mixtures for inter-response times, and Gaussian plus ramp models for peak procedure data, among others. For more details, refer to Alcala et al. (2023) <doi:10.31234/osf.io/8aq2j>.
Maintained by Emmanuel Alcala. Last updated 1 months ago.
7.7 match 4.00 scorelbelzile
mev:Modelling of Extreme Values
Various tools for the analysis of univariate, multivariate and functional extremes. Exact simulation from max-stable processes [Dombry, Engelke and Oesting (2016) <doi:10.1093/biomet/asw008>, R-Pareto processes for various parametric models, including Brown-Resnick (Wadsworth and Tawn, 2014, <doi:10.1093/biomet/ast042>) and Extremal Student (Thibaud and Opitz, 2015, <doi:10.1093/biomet/asv045>). Threshold selection methods, including Wadsworth (2016) <doi:10.1080/00401706.2014.998345>, and Northrop and Coleman (2014) <doi:10.1007/s10687-014-0183-z>. Multivariate extreme diagnostics. Estimation and likelihoods for univariate extremes, e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>.
Maintained by Leo Belzile. Last updated 5 months ago.
extreme-value-statisticslikelihood-functionsmax-stablesimulationthreshold-selectionopenblascppopenmp
3.6 match 13 stars 8.23 score 94 scripts 4 dependents
ekstroem
MethComp:Analysis of Agreement in Method Comparison Studies
Methods (standard and advanced) for analysis of agreement between measurement methods. These cover Bland-Altman plots, Deming regression, Lin's Total deviation index, and difference-on-average regression. See Carstensen B. (2010) "Comparing Clinical Measurement Methods: A Practical Guide (Statistics in Practice)" <doi:10.1002/9780470683019> for more information.
Maintained by Claus Thorn Ekstrøm. Last updated 5 months ago.
6.4 match 1 stars 4.63 score 86 scripts
mums2
mpactr:Correction of Preprocessed MS Data
An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) <doi:10.1021/acs.analchem.2c04632>). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.
Maintained by Patrick Schloss. Last updated 2 days ago.
5.3 match 1 stars 5.56 score 4 scripts
cshs-hydrology
CSHShydRology:Canadian Hydrological Analyses
A collection of user submitted functions to aid in the analysis of hydrological data.
Maintained by Kevin Shook. Last updated 3 years ago.
5.5 match 4 stars 5.26 score 23 scripts
maialba3
LipidMS:Lipid Annotation for LC-MS/MS DDA or DIA Data
Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.
Maintained by M Isabel Alcoriza-Balaguer. Last updated 7 months ago.
5.5 match 2 stars 5.33 score 12 scripts 1 dependents
martin3141
spant:MR Spectroscopy Analysis Tools
Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Maintained by Martin Wilson. Last updated 30 days ago.
brainmrimrsmrshubspectroscopyfortran
3.4 match 24 stars 8.55 score 81 scripts
jpquast
protti:Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Maintained by Jan-Philipp Quast. Last updated 5 months ago.
data-analysislip-msmass-spectrometryomicsproteinproteomicssystems-biology
3.4 match 61 stars 8.58 score 83 scripts
khliland
baseline:Baseline Correction of Spectra
Collection of baseline correction algorithms, along with a framework and a Tcl/Tk enabled GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Maintained by Kristian Hovde Liland. Last updated 10 months ago.
4.0 match 9 stars 7.08 score 74 scripts 12 dependentscran
monitoR:Acoustic Template Detection in R
Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.
Maintained by Sasha D. Hafner. Last updated 7 years ago.
7.2 match 3 stars 3.95 score 5 dependents
ilapros
winfapReader:Interact with Peak Flow Data in the United Kingdom
Obtain information on peak flow data from the National River Flow Archive (NRFA) in the United Kingdom, either from the Peak Flow Dataset files <https://nrfa.ceh.ac.uk/peak-flow-dataset> once these have been downloaded to the user's computer or using the NRFA's API. These files are in a format suitable for direct use in the 'WINFAP' software, hence the name of the package.
Maintained by Ilaria Prosdocimi. Last updated 9 months ago.
7.1 match 2 stars 4.00 score 5 scripts
sarahgoslee-usda
VFS:Vegetated Filter Strip and Erosion Model
Empirical models for runoff, erosion, and phosphorus loss across a vegetated filter strip, given slope, soils, climate, and vegetation (Gall et al., 2018) <doi:10.1007/s00477-017-1505-x>. It also includes functions for deriving climate parameters from measured daily weather data, and for simulating rainfall. Models implemented include MUSLE (Williams, 1975) and APLE (Vadas et al., 2009 <doi:10.2134/jeq2008.0337>).
Maintained by Sarah Goslee. Last updated 3 years ago.
5.1 match 1 stars 5.56 score 36 scriptsbioc
clippda:A package for the clinical proteomic profiling data analysis
Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.
Maintained by Stephen Nyangoma. Last updated 5 months ago.
proteomicsonechannelpreprocessingdifferentialexpressionmultiplecomparison
8.5 match 3.30 score 2 scriptsbioc
CAGEfightR:Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.
Maintained by Malte Thodberg. Last updated 5 months ago.
softwaretranscriptioncoveragegeneexpressiongeneregulationpeakdetectiondataimportdatarepresentationtranscriptomicssequencingannotationgenomebrowsersnormalizationpreprocessingvisualization
3.6 match 8 stars 7.46 score 67 scripts 1 dependentsbioc
MassArray:Analytical Tools for MassArray Data
This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.
Maintained by Reid F. Thompson. Last updated 5 months ago.
immunooncologydnamethylationsnpmassspectrometrygeneticsdataimportvisualization
6.3 match 4.30 score 1 scriptsbioc
tomoda:Tomo-seq data analysis
This package provides many easy-to-use methods to analyze and visualize tomo-seq data. The tomo-seq technique is based on cryosectioning of tissue and performing RNA-seq on consecutive sections. (Reference: Kruse F, Junker JP, van Oudenaarden A, Bakkers J. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods Cell Biol. 2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main purpose of the package is to find zones with similar transcriptional profiles and spatially expressed genes in a tomo-seq sample. Several visulization functions are available to create easy-to-modify plots.
Maintained by Wendao Liu. Last updated 5 months ago.
geneexpressionsequencingrnaseqtranscriptomicsspatialclusteringvisualization
6.7 match 4.00 score 2 scriptscran
extRemes:Extreme Value Analysis
General functions for performing extreme value analysis. In particular, allows for inclusion of covariates into the parameters of the extreme-value distributions, as well as estimation through MLE, L-moments, generalized (penalized) MLE (GMLE), as well as Bayes. Inference methods include parametric normal approximation, profile-likelihood, Bayes, and bootstrapping. Some bivariate functionality and dependence checking (e.g., auto-tail dependence function plot, extremal index estimation) is also included. For a tutorial, see Gilleland and Katz (2016) <doi: 10.18637/jss.v072.i08> and for bootstrapping, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Maintained by Eric Gilleland. Last updated 4 months ago.
7.1 match 2 stars 3.75 score 5 dependentsbioc
GenomicPlot:Plot profiles of next generation sequencing data in genomic features
Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. 'GenomicPlot' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.
Maintained by Shuye Pu. Last updated 1 months ago.
alternativesplicingchipseqcoveragegeneexpressionrnaseqsequencingsoftwaretranscriptionvisualizationannotation
4.7 match 3 stars 5.62 score 4 scriptsbioc
nucleR:Nucleosome positioning package for R
Nucleosome positioning for Tiling Arrays and NGS experiments.
Maintained by Alba Sala. Last updated 5 months ago.
nucleosomepositioningcoveragechipseqmicroarraysequencinggeneticsqualitycontroldataimport
5.0 match 5.32 score 21 scriptsbioc
CNAnorm:A normalization method for Copy Number Aberration in cancer samples
Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.
Maintained by Stefano Berri. Last updated 5 months ago.
copynumbervariationsequencingcoveragenormalizationwholegenomednaseqgenomicvariationfortran
6.2 match 4.30 score 6 scriptsbioc
BasicSTARRseq:Basic peak calling on STARR-seq data
Basic peak calling on STARR-seq data based on a method introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17.
Maintained by Annika Buerger. Last updated 5 months ago.
peakdetectiongeneregulationfunctionalpredictionfunctionalgenomicscoverage
8.0 match 3.30 score 1 scriptspaulnorthrop
revdbayes:Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis
Provides functions for the Bayesian analysis of extreme value models. The 'rust' package <https://cran.r-project.org/package=rust> is used to simulate a random sample from the required posterior distribution. The functionality of 'revdbayes' is similar to the 'evdbayes' package <https://cran.r-project.org/package=evdbayes>, which uses Markov Chain Monte Carlo ('MCMC') methods for posterior simulation. In addition, there are functions for making inferences about the extremal index, using the models for threshold inter-exceedance times of Suveges and Davison (2010) <doi:10.1214/09-AOAS292> and Holesovsky and Fusek (2020) <doi:10.1007/s10687-020-00374-3>. Also provided are d,p,q,r functions for the Generalised Extreme Value ('GEV') and Generalised Pareto ('GP') distributions that deal appropriately with cases where the shape parameter is very close to zero.
Maintained by Paul J. Northrop. Last updated 7 months ago.
analysisbayesianextremeextreme-value-statisticsextremesgeneralized-pareto-distributiongevinferencenhpppoint-processposteriorpredictivercppvalueopenblascpp
3.4 match 4 stars 7.62 score 58 scripts 4 dependents
sperfu
findGSEP:Estimate Genome Size of Polyploid Species Using k-Mer Frequencies
Provides tools to estimate the genome size of polyploid species using k-mer frequencies. This package includes functions to process k-mer frequency data and perform genome size estimation by fitting k-mer frequencies with a normal distribution model. It supports handling of complex polyploid genomes and offers various options for customizing the estimation process. The basic method 'findGSE' is detailed in Sun, Hequan, et al. (2018) <doi:10.1093/bioinformatics/btx637>.
Maintained by Laiyi Fu. Last updated 8 months ago.
5.3 match 3 stars 4.88 score 1 scriptsbioc
cosmiq:cosmiq - COmbining Single Masses Into Quantities
cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.
Maintained by David Fischer. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
5.8 match 4.48 score 2 scriptstdhock
PeakSegDisk:Disk-Based Constrained Change-Point Detection
Disk-based implementation of Functional Pruning Optimal Partitioning with up-down constraints <doi:10.18637/jss.v101.i10> for single-sample peak calling (independently for each sample and genomic problem), can handle huge data sets (10^7 or more).
Maintained by Toby Dylan Hocking. Last updated 6 months ago.
5.6 match 4 stars 4.65 score 37 scripts
drg-123
NSM3:Functions and Datasets to Accompany Hollander, Wolfe, and Chicken - Nonparametric Statistical Methods, Third Edition
Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Maintained by Grant Schneider. Last updated 4 months ago.
6.8 match 1 stars 3.77 score 115 scripts 1 dependents
jonathanlees
RSEIS:Seismic Time Series Analysis Tools
Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Maintained by Jonathan M. Lees. Last updated 6 months ago.
6.0 match 3 stars 4.27 score 262 scripts 4 dependents
pbiecek
ddst:Data Driven Smooth Tests
Smooth tests are data driven (alternative hypothesis is dynamically selected based on data). In this package you will find two groups of smooth of test: goodness-of-fit tests and nonparametric tests for comparing distributions. Among goodness-of-fit tests there are tests for exponent, Gaussian, Gumbel and uniform distribution. Among nonparametric tests there are tests for stochastic dominance, k-sample test, test with umbrella alternatives and test for change-point problems.
Maintained by Przemyslaw Biecek. Last updated 2 years ago.
data-drivensmooth-teststatisticstest
4.9 match 6 stars 5.26 score 6 scripts 2 dependents
smoeding
usl:Analyze System Scalability with the Universal Scalability Law
The Universal Scalability Law (Gunther 2007) <doi:10.1007/978-3-540-31010-5> is a model to predict hardware and software scalability. It uses system capacity as a function of load to forecast the scalability for the system.
Maintained by Stefan Moeding. Last updated 2 years ago.
scalabilityuniversal-scalability-lawusl
4.0 match 36 stars 6.32 score 117 scriptsbioc
simPIC:simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
simPIC is a package for simulating single-cell ATAC-seq count data. It provides a user-friendly, well documented interface for data simulation. Functions are provided for parameter estimation, realistic scATAC-seq data simulation, and comparing real and simulated datasets.
Maintained by Sagrika Chugh. Last updated 5 months ago.
singlecellatacseqsoftwaresequencingimmunooncologydataimport
5.6 match 4.54 score 3 scriptscran
Fragman:Fragment Analysis in R
Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Maintained by Giovanny Covarrubias-Pazaran. Last updated 7 years ago.
9.6 match 5 stars 2.65 score 1 dependentsbioc
metaMS:MS-based metabolomics annotation pipeline
MS-based metabolomics data processing and compound annotation pipeline.
Maintained by Yann Guitton. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
3.4 match 15 stars 7.50 score 15 scriptsbioc
openCyto:Hierarchical Gating Pipeline for flow cytometry data
This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.
Maintained by Mike Jiang. Last updated 5 months ago.
immunooncologyflowcytometrydataimportpreprocessingdatarepresentationcpp
3.3 match 7.62 score 404 scripts 1 dependentsbioc
TRESS:Toolbox for mRNA epigenetics sequencing analysis
This package is devoted to analyzing MeRIP-seq data. Current functionalities include 1. detect transcriptome wide m6A methylation regions 2. detect transcriptome wide differential m6A methylation regions.
Maintained by Zhenxing Guo. Last updated 5 months ago.
epigeneticsrnaseqpeakdetectiondifferentialmethylation
7.1 match 3.48 score 5 scripts 1 dependentsbioc
sarks:Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains
Suffix Array Kernel Smoothing (see https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797), or SArKS, identifies sequence motifs whose presence correlates with numeric scores (such as differential expression statistics) assigned to the sequences (such as gene promoters). SArKS smooths over sequence similarity, quantified by location within a suffix array based on the full set of input sequences. A second round of smoothing over spatial proximity within sequences reveals multi-motif domains. Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.
Maintained by Dennis Wylie. Last updated 5 months ago.
motifdiscoverygeneregulationgeneexpressiontranscriptomicsrnaseqdifferentialexpressionfeatureextractionopenjdk
5.2 match 3 stars 4.78 score 3 scripts
roaldarbol
animovement:An R toolbox for analysing animal movement across space and time
An R toolbox for analysing animal movement across space and time.
Maintained by Mikkel Roald-Arbøl. Last updated 2 months ago.
animal-behaviouranimal-movementneuroethologyneuroscience
5.1 match 10 stars 4.81 score 8 scriptsethanbass
chromConverter:Chromatographic File Converter
Reads chromatograms from binary formats into R objects. Currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions', 'ThermoRaw', and 'Varian Workstation' files as well as various text-based formats. In addition to its internal parsers, chromConverter contains bindings to parsers in external libraries, such as 'Aston' <https://github.com/bovee/aston>, 'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>, and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.
Maintained by Ethan Bass. Last updated 10 days ago.
cheminformaticschromatographyfair-datagc-fidhplchplc-dadhplc-uvmetabolomicsmetabolomics-dataopen-dataopen-science
3.9 match 33 stars 6.35 score 16 scripts 2 dependentsbioc
CluMSID:Clustering of MS2 Spectra for Metabolite Identification
CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.
Maintained by Tobias Depke. Last updated 5 months ago.
metabolomicspreprocessingclustering
4.1 match 10 stars 6.04 score 22 scripts
thomasp85
densityClust:Clustering by Fast Search and Find of Density Peaks
An improved implementation (based on k-nearest neighbors) of the density peak clustering algorithm, originally described by Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle large datasets (> 100,000 samples) very efficiently. It was initially implemented by Thomas Lin Pedersen, with inputs from Sean Hughes and later improved by Xiaojie Qiu to handle large datasets with kNNs.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
3.4 match 153 stars 7.14 score 75 scripts
knausb
vcfR:Manipulate and Visualize VCF Data
Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.
Maintained by Brian J. Knaus. Last updated 22 days ago.
genomicspopulation-geneticspopulation-genomicsrcppvcf-datavisualizationzlibcpp
1.8 match 254 stars 13.59 score 3.1k scripts 19 dependentsidslme
IDSL.CSA:Composite Spectra Analysis (CSA) for High-Resolution Mass Spectrometry Analyses
A fragmentation spectra detection pipeline for high-throughput LC/HRMS data processing using peaklists generated by the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120>. The 'IDSL.CSA' package can deconvolute fragmentation spectra from Composite Spectra Analysis (CSA), Data Dependent Acquisition (DDA) analysis, and various Data-Independent Acquisition (DIA) methods such as MS^E, All-Ion Fragmentation (AIF) and SWATH-MS analysis. The 'IDSL.CSA' package was introduced in <doi:10.1021/acs.analchem.3c00376>.
Maintained by Dinesh Barupal. Last updated 2 years ago.
composite-spectra-analysiscsadata-dependent-acquisitiondata-independent-acquisitionddadiamass-spectrometrymetabolomicsmetabolomics-pipelinesmall-moleculespectral-entropy
7.1 match 5 stars 3.40 scorebioc
squallms:Speedy quality assurance via lasso labeling for LC-MS data
squallms is a Bioconductor R package that implements a "semi-labeled" approach to untargeted mass spectrometry data. It pulls in raw data from mass-spec files to calculate several metrics that are then used to label MS features in bulk as high or low quality. These metrics of peak quality are then passed to a simple logistic model that produces a fully-labeled dataset suitable for downstream analysis.
Maintained by William Kumler. Last updated 5 months ago.
massspectrometrymetabolomicsproteomicslipidomicsshinyappsclassificationclusteringfeatureextractionprincipalcomponentregressionpreprocessingqualitycontrolvisualization
4.7 match 3 stars 5.13 score 5 scripts
rstudio
keras3:R Interface to 'Keras'
Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.
Maintained by Tomasz Kalinowski. Last updated 4 days ago.
1.8 match 845 stars 13.57 score 264 scripts 2 dependentsbioc
PIPETS:Poisson Identification of PEaks from Term-Seq data
PIPETS provides statistically robust analysis for 3'-seq/term-seq data. It utilizes a sliding window approach to apply a Poisson Distribution test to identify genomic positions with termination read coverage that is significantly higher than the surrounding signal. PIPETS then condenses proximal signal and produces strand specific results that contain all significant termination peaks.
Maintained by Quinlan Furumo. Last updated 5 months ago.
sequencingtranscriptiongeneregulationpeakdetectiongeneticstranscriptomicscoverage
6.2 match 3.85 score 2 scripts
billdenney
PKNCA:Perform Pharmacokinetic Non-Compartmental Analysis
Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.
Maintained by Bill Denney. Last updated 16 days ago.
ncanoncompartmental-analysispharmacokinetics
1.9 match 73 stars 12.61 score 214 scripts 4 dependents
jakobbossek
smoof:Single and Multi-Objective Optimization Test Functions
Provides generators for a high number of both single- and multi- objective test functions which are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.
Maintained by Jakob Bossek. Last updated 1 years ago.
benchmark-functionsmulti-objective-optimizationsingle-objective-optimizationcpp
2.8 match 36 stars 8.54 score 261 scripts 9 dependentsbioc
crisprViz:Visualization Functions for CRISPR gRNAs
Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.
Maintained by Jean-Philippe Fortin. Last updated 5 months ago.
crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-analysiscrispr-designgrnagrna-sequencegrna-sequencessgrnasgrna-designvisualization
3.8 match 7 stars 6.23 score 6 scripts 2 dependents
myles-lewis
locuszoomr:Gene Locus Plot with Gene Annotations
Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Maintained by Myles Lewis. Last updated 13 days ago.
3.1 match 40 stars 7.43 score 50 scriptsbioc
MSstatsPTM:Statistical Characterization of Post-translational Modifications
MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.
Maintained by Devon Kohler. Last updated 4 months ago.
immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolpost-translational-modificationcpp
2.9 match 10 stars 7.98 score 36 scripts 2 dependents
r-lib
covr:Test Coverage for Packages
Track and report code coverage for your package and (optionally) upload the results to a coverage service like 'Codecov' <https://about.codecov.io> or 'Coveralls' <https://coveralls.io>. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.
Maintained by Jim Hester. Last updated 1 months ago.
codecovcoveragecoverage-reporttravis-ci
1.5 match 337 stars 15.25 score 2.3k scripts 9 dependentsbioc
ChIPseqR:Identifying Protein Binding Sites in High-Throughput Sequencing Data
ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.
Maintained by Peter Humburg. Last updated 5 months ago.
4.9 match 4.70 score 1 scripts
tpetzoldt
simecol:Simulation of Ecological (and Other) Dynamic Systems
An object oriented framework to simulate ecological (and other) dynamic systems. It can be used for differential equations, individual-based (or agent-based) and other models as well. It supports structuring of simulation scenarios (to avoid copy and paste) and aims to improve readability and re-usability of code.
Maintained by Thomas Petzoldt. Last updated 7 months ago.
4.8 match 4.76 score 190 scripts
schochastics
networkdata:Repository of Network Datasets
The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.
Maintained by David Schoch. Last updated 12 months ago.
4.5 match 143 stars 5.01 score 143 scripts
byandell-sysgen
qtl2ggplot:Data Visualization for QTL Experiments
Functions to plot QTL (quantitative trait loci) analysis results and related diagnostics. Part of 'qtl2', an upgrade of the 'qtl' package to better handle high-dimensional data and complex cross designs.
Maintained by Brian S Yandell. Last updated 1 years ago.
5.7 match 5 stars 3.93 score 17 scripts
rformassspectrometry
Chromatograms:Infrastructure for Chromatographic Mass Spectrometry Data
The Chromatograms packages defines a efficient infrastructure for storing and handling of chromatographic mass spectrometry data. It provides different implementations of *backends* to store and represent the data. Such backends can be optimized for small memory footprint or fast data access/processing. A lazy evaluation queue and chunk-wise processing capabilities ensure efficient analysis of also very large data sets.
Maintained by Philippine Louail. Last updated 26 days ago.
infrastructureproteomicsmassspectrometrymetabolomics
5.3 match 1 stars 4.15 score 3 scripts
epiverse-trace
epidemics:Composable Epidemic Scenario Modelling
A library of compartmental epidemic models taken from the published literature, and classes to represent affected populations, public health response measures including non-pharmaceutical interventions on social contacts, non-pharmaceutical and pharmaceutical interventions that affect disease transmissibility, vaccination regimes, and disease seasonality, which can be combined to compose epidemic scenario models.
Maintained by Rosalind Eggo. Last updated 9 months ago.
decision-supportepidemic-modellingepidemic-simulationsepidemiologyepiverseinfectious-disease-dynamicsmodel-librarynon-pharmaceutical-interventionsrcpprcppeigenscenario-analysisvaccinationcpp
3.0 match 9 stars 7.48 score 59 scripts
bcgov
fasstr:Analyze, Summarize, and Visualize Daily Streamflow Data
The Flow Analysis Summary Statistics Tool for R, 'fasstr', provides various functions to tidy and screen daily stream discharge data, calculate and visualize various summary statistics and metrics, and compute annual trending and volume frequency analyses. It features useful function arguments for filtering of and handling dates, customizing data and metrics, and the ability to pull daily data directly from the Water Survey of Canada hydrometric database (<https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>).
Maintained by Jon Goetz. Last updated 6 months ago.
bcgovforfrequency-analysishydathydrologystreamflowsummary-statisticstrendswater
2.9 match 57 stars 7.48 score 89 scriptsbioc
m6Aboost:m6Aboost
This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the m6Aboost model. The miCLIP2 data should be stored in a GRanges object. More details can be found in the vignette.
Maintained by You Zhou. Last updated 5 months ago.
sequencingepigeneticsgeneticsexperimenthubsoftware
5.1 match 2 stars 4.30 score 5 scripts
bastian-schaefer
DCSmooth:Nonparametric Regression and Bandwidth Selection for Spatial Models
Nonparametric smoothing techniques for data on a lattice and functional time series. Smoothing is done via kernel regression or local polynomial regression, a bandwidth selection procedure based on an iterative plug-in algorithm is implemented. This package allows for modeling a dependency structure of the error terms of the nonparametric regression model. Methods used in this paper are described in Feng/Schaefer (2021) <https://ideas.repec.org/p/pdn/ciepap/144.html>, Schaefer/Feng (2021) <https://ideas.repec.org/p/pdn/ciepap/143.html>.
Maintained by Bastian Schaefer. Last updated 3 years ago.
8.0 match 2.70 score 5 scripts
sentometricsresearch
sentometrics:An Integrated Framework for Textual Sentiment Time Series Aggregation and Prediction
Optimized prediction based on textual sentiment, accounting for the intrinsic challenge that sentiment can be computed and pooled across texts and time in various ways. See Ardia et al. (2021) <doi:10.18637/jss.v099.i02>.
Maintained by Samuel Borms. Last updated 4 years ago.
nlppredictionsentiment-analysistext-miningtime-seriesopenblascppopenmp
3.5 match 83 stars 6.09 score 49 scripts
spang-lab
metabodecon:Deconvolution and Alignment of 1d NMR Spectra
A framework for deconvolution, alignment and postprocessing of 1-dimensional (1d) nuclear magnetic resonance (NMR) spectra, resulting in a data matrix of aligned signal integrals. The deconvolution part uses the algorithm described in Koh et al. (2009) <doi:10.1016/j.jmr.2009.09.003>. The alignment part is based on functions from the 'speaq' package, described in Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018> and Vu et al. (2011) <doi:10.1186/1471-2105-12-405>. A detailed description and evaluation of an early version of the package, 'MetaboDecon1D v0.2.2', can be found in Haeckl et al. (2021) <doi:10.3390/metabo11070452>.
Maintained by Tobias Schmidt. Last updated 6 days ago.
5.9 match 2 stars 3.60 score 2 scripts
bioc
RCAS:RNA Centric Annotation System
RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome. RCAS produces in-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features (exons, introns, 5'/3' UTR regions, exon-intron boundaries, promoter regions). Moreover, RCAS can carry out functional enrichment analyses and discriminative motif discovery.
Maintained by Bora Uyar. Last updated 5 months ago.
softwaregenetargetmotifannotationmotifdiscoverygotranscriptomicsgenomeannotationgenesetenrichmentcoverage
3.3 match 6.32 score 29 scripts 1 dependentsbioc
consensusSeekeR:Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. In genomic analysis where feature identification generates a position value surrounded by a genomic range, such as ChIP-Seq peaks and nucleosome positions, the replication of an experiment may result in slight differences between predicted values. This package enables the conciliation of the results into consensus regions.
Maintained by Astrid Deschênes. Last updated 5 months ago.
biologicalquestionchipseqgeneticsmultiplecomparisontranscriptionpeakdetectionsequencingcoveragechip-seq-analysisgenomic-data-analysisnucleosome-positioning
3.9 match 1 stars 5.26 score 5 scripts 1 dependentsr-forge
lokern:Kernel Regression Smoothing with Local or Global Plug-in Bandwidth
Kernel regression smoothing with adaptive local or global plug-in bandwidth selection.
Maintained by Martin Maechler. Last updated 3 months ago.
3.6 match 5.64 score 64 scripts 5 dependents
mkruijver
simDNAmixtures:Simulate Forensic DNA Mixtures
Mixed DNA profiles can be sampled according to models for probabilistic genotyping. Peak height variability is modelled using a log normal distribution or a gamma distribution. Sample contributors may be related according to a pedigree.
Maintained by Maarten Kruijver. Last updated 3 months ago.
4.0 match 5.04 score 9 scripts