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

vlpb3/faradr
  • * DESCRIPTION

Size: 4.58 MB - Last synced: 26 days ago - Pushed: over 7 years 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