Showing 19 of total 19 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 16 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
196 stars 14.31 score 984 scripts 11 dependentsbioc
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 23 days ago.
infrastructureproteomicsmassspectrometrymetabolomicsbioconductorhacktoberfestmass-spectrometry
41 stars 13.01 score 254 scripts 35 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 16 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
131 stars 12.76 score 772 scripts 36 dependents
spatstat
spatstat.geom:Geometrical Functionality of the 'spatstat' Family
Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)
Maintained by Adrian Baddeley. Last updated 5 days ago.
classes-and-objectsdistance-calculationgeometrygeometry-processingimagesmensurationplottingpoint-patternsspatial-dataspatial-data-analysis
7 stars 12.14 score 241 scripts 229 dependentsbioc
ShortRead:FASTQ input and manipulation
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
8 stars 12.08 score 1.8k scripts 49 dependentsbioc
affy:Methods for Affymetrix Oligonucleotide Arrays
The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
Maintained by Robert D. Shear. Last updated 3 months ago.
microarrayonechannelpreprocessing
11.12 score 2.5k scripts 98 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
62 stars 11.06 score 180 scripts 44 dependents
bioc
oligo:Preprocessing tools for oligonucleotide arrays
A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
Maintained by Benilton Carvalho. Last updated 22 days ago.
microarrayonechanneltwochannelpreprocessingsnpdifferentialexpressionexonarraygeneexpressiondataimportzlib
3 stars 10.42 score 528 scripts 10 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
48 stars 10.32 score 200 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
8 stars 9.36 score 4 scripts 188 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
10 stars 6.04 score 22 scriptsbioc
MsBackendRawFileReader:Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
implements a MsBackend for the Spectra package using Thermo Fisher Scientific's NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package Methods defined in this package are supposed to extend the Spectra Bioconductor package.
Maintained by Christian Panse. Last updated 5 months ago.
massspectrometryproteomicsmetabolomics
5 stars 5.94 score 5 scriptsbioc
MsBackendSql:SQL-based Mass Spectrometry Data Backend
SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.
Maintained by Johannes Rainer. Last updated 13 days ago.
infrastructuremassspectrometrymetabolomicsdataimportproteomics
4 stars 5.41 score 16 scripts
fcheysson
hawkesbow:Estimation of Hawkes Processes from Binned Observations
Implements an estimation method for Hawkes processes when count data are only observed in discrete time, using a spectral approach derived from the Bartlett spectrum, see Cheysson and Lang (2020) <arXiv:2003.04314>. Some general use functions for Hawkes processes are also included: simulation of (in)homogeneous Hawkes process, maximum likelihood estimation, residual analysis, etc.
Maintained by Felix Cheysson. Last updated 1 years ago.
7 stars 4.54 score 4 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 1 months ago.
infrastructureproteomicsmassspectrometrymetabolomics
1 stars 4.15 score 3 scripts
kbroman
xoi:Tools for Analyzing Crossover Interference
Analysis of crossover interference in experimental crosses, particularly regarding the gamma model. See, for example, Broman and Weber (2000) <doi:10.1086/302923>.
Maintained by Karl W Broman. Last updated 2 years ago.
4 stars 3.76 score 29 scripts
tagteam
SmoothHazard:Estimation of Smooth Hazard Models for Interval-Censored Data
Estimation of two-state (survival) models and irreversible illness- death models with possibly interval-censored, left-truncated and right-censored data. Proportional intensities regression models can be specified to allow for covariates effects separately for each transition. We use either a parametric approach with Weibull baseline intensities or a semi-parametric approach with M-splines approximation of baseline intensities in order to obtain smooth estimates of the hazard functions. Parameter estimates are obtained by maximum likelihood in the parametric approach and by penalized maximum likelihood in the semi-parametric approach.
Maintained by Thomas Alexander Gerds. Last updated 12 months ago.
2.73 score 36 scripts
mojaveazure
mamisc:Miscellaneous Functions by Paul Hoffman
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
Maintained by Paul Hoffman. Last updated 2 years ago.
1.70 score