Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
Package Usage: cran: IRanges
View more package details: https://packages.ecosyste.ms/registries/cran.r-project.org/packages/IRanges
Dependent Repos 1,227
jorainer/ensembldb
This is the ensembldb development repository.- >= 2.13.24 DESCRIPTION
Size: 6.57 MB - Last synced: 4 days ago - Pushed: 21 days ago
soccin/seqCNA
Copy number analysis of shallow whole genome sequencing- * DESCRIPTION
- * Rlib/seqDNAcopy/DESCRIPTION
Size: 7.91 MB - Last synced: 4 months ago - Pushed: 4 months ago
elsasserlab/labcode
Utils to perform frequent data analyses in the lab.- * elsasserlib/DESCRIPTION
Size: 17.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago
MoseleyBioinformaticsLab/ScanCentricPeakCharacterization
R package for scan-centric, frequency based peak characterization of mass spectrometry- * DESCRIPTION
Size: 765 MB - Last synced: about 1 month ago - Pushed: about 1 month ago
jimhester/GenomicRanges 📦
- >= 2.1.28 DESCRIPTION
Size: 8.35 MB - Last synced: about 1 year ago - Pushed: about 9 years ago
TRON-Bioinformatics/splice2neo
R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes- * DESCRIPTION
Size: 11.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago
rscharpf/VanillaICE-release
- >= 1.14.0 DESCRIPTION
Size: 1.24 MB - Last synced: about 1 year ago - Pushed: almost 9 years ago
samabs/conliga
Probabilistic inference of somatic copy number alterations using repeat DNA (FAST-SeqS)- >= 2.4.7 DESCRIPTION
Size: 5.1 MB - Last synced: about 1 year ago - Pushed: over 5 years ago
microbiome/mia
Microbiome analysis- * DESCRIPTION
Size: 20.8 MB - Last synced: about 21 hours ago - Pushed: about 22 hours ago
Wedge-lab/dpclust3p
Dirichlet Process Clustering Pre-Processing Pipeline- * DESCRIPTION
Size: 268 KB - Last synced: 9 months ago - Pushed: 10 months ago
fmicompbio/monaLisa
binned motif enrichment analysis and visualisation- * DESCRIPTION
Size: 44.9 MB - Last synced: 5 days ago - Pushed: 5 days ago
chrisamiller/copyCat
a parallel R package for detecting copy-number alterations from short sequencing reads- * DESCRIPTION
Size: 14.9 MB - Last synced: 7 months ago - Pushed: almost 3 years ago
clark-lab-robot/Repitools-git
A git version of our Repitools R package (the R-forge svn version will *always* be more up do date)- * pkg/Repitools/DESCRIPTION
- * pkg/Repitools/DESCRIPTION
Size: 3.12 MB - Last synced: 7 months ago - Pushed: almost 13 years ago
gschofl/genoslideR
Handle multiple genomic alignments with annotation in R- * DESCRIPTION
Size: 2.71 MB - Last synced: about 1 year ago - Pushed: about 10 years ago
lgatto/MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics- >= 2.13.28 DESCRIPTION
Size: 96.6 MB - Last synced: 3 days ago - Pushed: 5 days ago
cassj/my_bioinfo_scripts
Just a dumping ground for an assortment of bioinformatics scripts in various states of disrepair.- * liftoveR/DESCRIPTION
Size: 57.4 MB - Last synced: about 1 year ago - Pushed: over 11 years ago
Simon-Coetzee/motifBreakR
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.- * DESCRIPTION
Size: 6.86 MB - Last synced: 11 days ago - Pushed: 11 days ago
jmacdon/methylation
Package for working with Illumina methylation arrays- * DESCRIPTION
Size: 196 KB - Last synced: 9 months ago - Pushed: over 8 years ago
rformassspectrometry/Spectra
Low level infrastructure to handle MS spectra- * DESCRIPTION
Size: 16.6 MB - Last synced: 6 days ago - Pushed: 6 days ago
FemeniasM/ExplorATEproject
R package to explore active transposable elements with RNA-seq data- * DESCRIPTION
Size: 4.39 MB - Last synced: 11 months ago - Pushed: over 1 year ago
tidyomics/plyranges
A grammar of genomic data transformation- >= 2.12.0 DESCRIPTION
Size: 3.25 MB - Last synced: 10 days ago - Pushed: 24 days ago
PhanstielLab/plotgardener
- * DESCRIPTION
Size: 126 MB - Last synced: 4 days ago - Pushed: 19 days ago
robinweide/GENOVA
GENome Organisation Visual Analytics- * DESCRIPTION
Size: 493 MB - Last synced: about 2 months ago - Pushed: about 2 months ago
ataudt/aneufinder
Find CNVs in single cell sequencing data.- * DESCRIPTION
Size: 35.9 MB - Last synced: 12 days ago - Pushed: about 1 year ago
vodkatad/MatrixRider
Calculate total affinity and occupancies for binding site matrices on a given sequence- * DESCRIPTION
Size: 97.7 KB - Last synced: 9 months ago - Pushed: almost 6 years ago
maize-genetics/rTASSEL
R front-end for TASSEL- * DESCRIPTION
Size: 205 MB - Last synced: 3 months ago - Pushed: 6 months ago
dingruofan/xQTLbiolinks
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs- * DESCRIPTION
Size: 58.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago
insightsengineering/hermes
Preprocessing, analyzing, and reporting of RNA-seq data- * DESCRIPTION
Size: 45.2 MB - Last synced: 6 days ago - Pushed: 7 days ago
ErasmusMC-CCBC/katdetectr
An R package for detection, characterization and visualization of kataegis.- >= 2.26.0 DESCRIPTION
Size: 1.3 MB - Last synced: 2 months ago - Pushed: 2 months ago
npcooley/SynExtend
Tools for working with synteny objects- * DESCRIPTION
Size: 19.2 MB - Last synced: 6 days ago - Pushed: 7 days ago
MalteThodberg/CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor- >= 2.12.0 DESCRIPTION
Size: 13.5 MB - Last synced: 10 days ago - Pushed: over 2 years ago
GreenleafLab/chromVAR
chromatin Variability Across Regions (of the genome!)- * DESCRIPTION
Size: 18.8 MB - Last synced: 3 months ago - Pushed: 6 months ago
thomasp85/FindMyFriends
Fast alignment-free pangenome creation and exploration- * DESCRIPTION
Size: 1.93 MB - Last synced: 7 months ago - Pushed: about 4 years ago
MalteThodberg/tidyGenomeBrowser
Easy genome browser figures using R / Bioconductor- >= 2.22.2 DESCRIPTION
Size: 1.42 MB - Last synced: 3 months ago - Pushed: 3 months ago
arsenew/methSeg
provide segmentation functions- * DESCRIPTION
Size: 8.76 MB - Last synced: about 1 year ago - Pushed: almost 9 years ago
jrboyd/seqsetvis
Allows general set comparisons with a focus on sets of genomic locations (ChIP-seq peaks primarily). The includes standard visualizations such as venn and euler diagrams but more powerfully of genomic signal pulled from bigwig files.- * DESCRIPTION
Size: 61 MB - Last synced: 17 days ago - Pushed: 17 days ago
welch-lab/liger
R package for integrating and analyzing multiple single-cell datasets- * DESCRIPTION
Size: 193 MB - Last synced: 18 days ago - Pushed: about 1 month ago
LieberInstitute/spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app- * DESCRIPTION
Size: 187 MB - Last synced: 3 days ago - Pushed: 3 days ago
sulab-wmu/scPagwas
Obtain trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with GWAS data- * DESCRIPTION
Size: 992 MB - Last synced: 12 days ago - Pushed: 12 days ago
griffithlab/GenVisR
Genome data visualizations- >= 2.7.5 DESCRIPTION
Size: 38 MB - Last synced: 22 days ago - Pushed: 22 days ago
BIMSBbioinfo/ciRcus
An R package for annotation of circular RNAs- * DESCRIPTION
Size: 72.3 MB - Last synced: 6 months ago - Pushed: about 4 years ago
kullrich/MSA2dist
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis- * DESCRIPTION
Size: 601 KB - Last synced: 11 days ago - Pushed: 11 days ago
kstreet13/VDJdive
For code related to T cell repertoire analysis- * DESCRIPTION
Size: 1.28 MB - Last synced: 4 days ago - Pushed: 12 months ago
tengfei/chromatoplots
- * DESCRIPTION
Size: 1.97 MB - Last synced: 22 days ago - Pushed: almost 11 years ago
mfansler/txcutr
R methods for generating truncated transcript annotations- * DESCRIPTION
Size: 68.4 KB - Last synced: 18 days ago - Pushed: 18 days ago
RockefellerUniversity/profileplyr
- * DESCRIPTION
Size: 9.27 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
velocyto-team/velocyto.R
RNA velocity estimation in R- * DESCRIPTION
Size: 1.72 MB - Last synced: 7 months ago - Pushed: 8 months ago
ShixiangWang/sigminer
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html- * DESCRIPTION
Size: 51 MB - Last synced: 22 days ago - Pushed: about 2 months ago
UMMS-Biocore/debrowser
Differential Count Data Analysis Toolbox- * DESCRIPTION
Size: 38.7 MB - Last synced: about 1 month ago - Pushed: 3 months ago
rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data- * DESCRIPTION
Size: 20.9 MB - Last synced: 21 days ago - Pushed: 22 days ago
msettles/rSFFreader
R packages for flow gram based sequence data Roche 454 and Ion Torrent- >= 1.15.42 DESCRIPTION
- * DESCRIPTION
Size: 4.35 MB - Last synced: about 2 months ago - Pushed: over 10 years ago
andrew-hipp/RADami
RADseq helper R package- * DESCRIPTION
Size: 136 KB - Last synced: 6 months ago - Pushed: 6 months ago
databio/GenomicDistributions
Calculate and plot distributions of genomic ranges- * DESCRIPTION
Size: 9.27 MB - Last synced: 9 days ago - Pushed: 9 days ago
rseng/rsepedia-analysis
Exploring clustering of research software encyclopedia entries- * _repos/github/HajkD/LTRpred/DESCRIPTION
- >= 2.12.0 _repos/github/LabTranslationalArchitectomics/riboWaltz/DESCRIPTION
- * _repos/github/ScialdoneLab/MitoHEAR/DESCRIPTION
- * _repos/github/ShixiangWang/sigminer/DESCRIPTION
- * _repos/github/pmoulos/metaseqR2/DESCRIPTION
Size: 433 MB - Last synced: 4 days ago - Pushed: 5 days ago
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq- * DESCRIPTION
Size: 367 MB - Last synced: 2 days ago - Pushed: 3 days ago
nullranges/nullranges
Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrapped ranges (bootRanges), or set of control ranges that are matched across one or more covariates (matchRanges).- * DESCRIPTION
Size: 26.5 MB - Last synced: 6 months ago - Pushed: 9 months ago
kokonech/InTAD
Correlation of epigenetic signals and genes in TADs/via loops- * DESCRIPTION
Size: 517 KB - Last synced: 7 months ago - Pushed: over 2 years ago
Bioconductor/AnnotationHub
Client for the Bioconductor AnnotationHub web resource- * DESCRIPTION
Size: 1.38 MB - Last synced: 4 days ago - Pushed: 5 days ago
drisso/archive-EDASeq
Archived version of EDASeq- >= 1.13.9 DESCRIPTION
Size: 190 KB - Last synced: 7 months ago - Pushed: over 7 years ago
RTCGA/RTCGA
Download, integration and visualizations of the variety & volume of TCGA data.- * DESCRIPTION
Size: 17.8 MB - Last synced: 5 days ago - Pushed: over 1 year ago
podpearson/pv
R package for analysis of Malariagen Plasmodium vivax data- * DESCRIPTION
Size: 246 KB - Last synced: about 1 year ago - Pushed: almost 11 years ago
BaderLab/netDx
R package with netDx software and data for examples- * DESCRIPTION
Size: 115 MB - Last synced: about 1 month ago - Pushed: about 1 year ago
ben-laufer/DMRichR
A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)- * DESCRIPTION
Size: 4.25 MB - Last synced: 7 months ago - Pushed: 7 months ago
rmflight/metabolomicsUtilities
useful utilities in processing metabolomics data- * DESCRIPTION
Size: 337 KB - Last synced: 6 months ago - Pushed: 6 months ago
Bioconductor/GenomicFeatures
Conveniently import and query gene models- >= 2.13.23 DESCRIPTION
Size: 45.7 MB - Last synced: 4 days ago - Pushed: 6 days ago
genomicsclass/ph525x
ph525x. functions only, no data- * DESCRIPTION
Size: 37.8 MB - Last synced: 9 months ago - Pushed: almost 2 years ago
CopenhagenCenterForGlycomics/Rgator
R tools for interacting with the Gator- * DESCRIPTION
Size: 252 KB - Last synced: about 1 month ago - Pushed: 2 months ago
cgplab/Rockermeth
A tool for discovering Differentially Methylated Regions- * DESCRIPTION
Size: 164 MB - Last synced: about 1 year ago - Pushed: about 2 years ago
MatthiasLienhard/qsea
QSEA bioconductor package- * DESCRIPTION
Size: 381 KB - Last synced: 7 months ago - Pushed: about 1 year ago
ttriche/regulatoR
R package to detect correlated changes across phenotypes by sparse filtered regression- * DESCRIPTION
Size: 2.19 MB - Last synced: 9 months ago - Pushed: about 11 years ago
genome/sciclone
An R package for inferring the subclonal architecture of tumors- * DESCRIPTION
Size: 13.8 MB - Last synced: 12 days ago - Pushed: 7 months ago
RGLab/HIV.db
HIV annotation database- * DESCRIPTION
Size: 1.36 MB - Last synced: about 1 year ago - Pushed: over 8 years ago
pkimes/spliceclust
visualization tools for exon/junction coverage- * DESCRIPTION
Size: 54.1 MB - Last synced: about 2 months ago - Pushed: over 4 years ago
jokergoo/InteractiveComplexHeatmap
Make Interactive Complex Heatmaps- * DESCRIPTION
Size: 7.44 MB - Last synced: 6 months ago - Pushed: 9 months ago
lgatto/Pbase
Manipluating and exploring protein and proteomics data- >= 2.13.11 DESCRIPTION
Size: 24.2 MB - Last synced: 7 months ago - Pushed: over 4 years ago
gschofl/porequal
Quality assessment of SAM/BAM-based multiple alignments- * DESCRIPTION
Size: 125 KB - Last synced: about 1 year ago - Pushed: over 9 years ago
lawremi/rtracklayer
R interface to genome annotation files and the UCSC genome browser- >= 2.13.13 DESCRIPTION
Size: 15.7 MB - Last synced: 2 days ago - Pushed: 3 days ago
jimhester/AllelicImbalance 📦
- * DESCRIPTION
Size: 21.1 MB - Last synced: about 1 year ago - Pushed: about 9 years ago
bheesink/ENCODER
ENCODER: DNA copy number detection from off-target sequence data- * ENCODER/DESCRIPTION
Size: 189 KB - Last synced: about 1 year ago - Pushed: over 9 years ago
chrisamiller/readDepth
R package for inferring copy number from read depth- * DESCRIPTION
Size: 38.1 KB - Last synced: 7 months ago - Pushed: over 1 year ago
andrespan/PkgedemoCDSB2022
- * s4demo-main/DESCRIPTION
Size: 3.91 KB - Last synced: 9 months ago - Pushed: almost 2 years ago
jorainer/GenomePlotR
- >= 1.10.0 DESCRIPTION
Size: 172 KB - Last synced: 9 months ago - Pushed: over 9 years ago
acidgenomics/r-acidexperiment
Toolkit to extend the functionality of SummarizedExperiment.- * DESCRIPTION
Size: 835 KB - Last synced: about 2 months ago - Pushed: about 2 months ago
acidgenomics/r-pipette
Pipette biological data in and out of R.- * DESCRIPTION
Size: 3.21 MB - Last synced: about 2 months ago - Pushed: about 2 months ago
gustaveroussy/EaCoN
Easy Copy Number !- * DESCRIPTION
Size: 3.1 MB - Last synced: about 1 year ago - Pushed: over 2 years ago
CTrierMaansson/DNAfusion
Identification of gene-fusions, including EML4-ALK- * DESCRIPTION
Size: 63.1 MB - Last synced: 10 days ago - Pushed: 6 months ago
plger/scDblFinder
Methods for detecting doublets in single-cell sequencing data- * DESCRIPTION
Size: 12.3 MB - Last synced: 16 days ago - Pushed: about 2 months ago
jsemple19/EMclassifieR
Package for classifying methylation matrices from reads into probabilistic classes with the expectation maximisation algorithm. Based on work by Kyriakos Schwartz- * DESCRIPTION
Size: 1.13 MB - Last synced: about 1 month ago - Pushed: over 1 year ago
vsbuffalo/tasselr
Some beta interfaces to Tassel's GBS data on HDF5- * DESCRIPTION
Size: 305 KB - Last synced: 21 days ago - Pushed: almost 9 years ago
PeeperLab/CopywriteR
DNA copy number detection from off-target sequence data- * DESCRIPTION
Size: 2.62 MB - Last synced: about 2 months ago - Pushed: almost 6 years ago
dpryan79/BBMeth
BBMeth: An R package for fitting methylation data with a beta-binomial model- * DESCRIPTION
Size: 176 KB - Last synced: 9 months ago - Pushed: over 9 years ago
nsheff/dipPeak
Kernel density estimator for DNase data.- * DESCRIPTION
Size: 171 KB - Last synced: 3 months ago - Pushed: almost 9 years ago