Showing 18 of total 18 results (show query)
bioc
nucleoSim:Generate synthetic nucleosome maps
This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.
Maintained by Astrid Deschênes. Last updated 5 months ago.
geneticssequencingsoftwarestatisticalmethodalignmentbioconductornucleosome-mapsnucleosomessimulationsimulatorsynthetic-nucleosomes
48.6 match 2 stars 5.00 score 8 scriptsbioc
RJMCMCNucleosomes:Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.
Maintained by Astrid Deschênes. Last updated 5 months ago.
biologicalquestionchipseqnucleosomepositioningsoftwarestatisticalmethodbayesiansequencingcoveragebayesian-t-mixturebioconductorc-plus-plusgenome-wide-profilingmultinomial-dirichlet-priornucleosome-positioningnucleosomesreversible-jump-mcmcgslcpp
49.2 match 4.30 score 1 scriptsbioc
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
29.7 match 1 stars 5.26 score 5 scripts 1 dependentsbioc
nucleR:Nucleosome positioning package for R
Nucleosome positioning for Tiling Arrays and NGS experiments.
Maintained by Alba Sala. Last updated 5 months ago.
nucleosomepositioningcoveragechipseqmicroarraysequencinggeneticsqualitycontroldataimport
25.0 match 5.32 score 21 scriptsbioc
NuPoP:An R package for nucleosome positioning prediction
NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.
Maintained by Ji-Ping Wang. Last updated 5 months ago.
geneticsvisualizationclassificationnucleosomepositioninghiddenmarkovmodelfortran
19.4 match 5.04 score 11 scriptsbioc
ATACseqQC:ATAC-seq Quality Control
ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.
Maintained by Jianhong Ou. Last updated 2 months ago.
sequencingdnaseqatacseqgeneregulationqualitycontrolcoveragenucleosomepositioningimmunooncology
12.8 match 7.12 score 146 scripts 1 dependentsbioc
nuCpos:An R package for prediction of nucleosome positions
nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (HBA) scores for a given 147-bp sequence. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. nuCpos continues to provide functions for HBA calculation.
Maintained by Hiroaki Kato. Last updated 5 months ago.
geneticsepigeneticsnucleosomepositioning
8.6 match 4.00 score 1 scriptsbioc
VplotR:Set of tools to make V-plots and compute footprint profiles
The pattern of digestion and protection from DNA nucleases such as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to infer the location of associated proteins. This package contains useful functions to analyze patterns of paired-end sequencing fragment density. VplotR facilitates the generation of V-plots and footprint profiles over single or aggregated genomic loci of interest.
Maintained by Jacques Serizay. Last updated 5 months ago.
nucleosomepositioningcoveragesequencingbiologicalquestionatacseqalignment
5.3 match 10 stars 5.64 score 11 scripts
waldronlab
SingleCellMultiModal:Integrating Multi-modal Single Cell Experiment datasets
SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see <https://doi.org/10.1371/journal.pcbi.1011324>.
Maintained by Marcel Ramos. Last updated 4 months ago.
experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073
2.9 match 17 stars 7.29 score 60 scriptsbioc
methylscaper:Visualization of Methylation Data
methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning.
Maintained by Bacher Rhonda. Last updated 5 months ago.
dnamethylationepigeneticssequencingvisualizationsinglecellnucleosomepositioning
3.3 match 1 stars 4.90 score 3 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.
1.9 match 184 stars 7.48 score 172 scriptsbioc
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.
2.5 match 4.70 score 1 scriptsbioc
SingleMoleculeFootprinting:Analysis tools for Single Molecule Footprinting (SMF) data
SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location.
Maintained by Guido Barzaghi. Last updated 28 days ago.
dnamethylationcoveragenucleosomepositioningdatarepresentationepigeneticsmethylseqqualitycontrolsequencing
1.7 match 2 stars 6.43 score 27 scriptsbioc
PING:Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data
Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.
Maintained by Renan Sauteraud. Last updated 5 months ago.
clusteringstatisticalmethodvisualizationsequencinggsl
2.8 match 4.00 score 7 scripts
fmicompbio
swissknife:Handy code shared in the FMI CompBio group
A collection of useful R functions performing various tasks that might be re-usable and worth sharing.
Maintained by Michael Stadler. Last updated 2 months ago.
1.8 match 8 stars 3.76 score 12 scriptsbioc
dinoR:Differential NOMe-seq analysis
dinoR tests for significant differences in NOMe-seq footprints between two conditions, using genomic regions of interest (ROI) centered around a landmark, for example a transcription factor (TF) motif. This package takes NOMe-seq data (GCH methylation/protection) in the form of a Ranged Summarized Experiment as input. dinoR can be used to group sequencing fragments into 3 or 5 categories representing characteristic footprints (TF bound, nculeosome bound, open chromatin), plot the percentage of fragments in each category in a heatmap, or averaged across different ROI groups, for example, containing a common TF motif. It is designed to compare footprints between two sample groups, using edgeR's quasi-likelihood methods on the total fragment counts per ROI, sample, and footprint category.
Maintained by Michaela Schwaiger. Last updated 5 months ago.
nucleosomepositioningepigeneticsmethylseqdifferentialmethylationcoveragetranscriptionsequencingsoftware
1.3 match 4.18 score 7 scriptsbioc
ChIPsim:Simulation of ChIP-seq experiments
A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.
Maintained by Peter Humburg. Last updated 5 months ago.
0.5 match 4.00 score 3 scriptsbioc
CoverageView:Coverage visualization package for R
This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome
Maintained by Ernesto Lowy. Last updated 5 months ago.
immunooncologyvisualizationrnaseqchipseqsequencingtechnologysoftware
0.5 match 2.78 score 5 scripts