Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
Package Usage: cran: BiocStyle
View more package details: https://packages.ecosyste.ms/registries/cran.r-project.org/packages/BiocStyle
Dependent Repos 1,739
jorainer/ensembldb
This is the ensembldb development repository.- * DESCRIPTION
Size: 6.57 MB - Last synced: 4 days ago - Pushed: 21 days ago
mil2041/netboxr
An R package to mark functional modules in the network analysis using data from pathwayCommons- * DESCRIPTION
Size: 48.7 MB - Last synced: 7 months ago - Pushed: 12 months ago
angelolab/FlowSOM Fork of SofieVG/FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry data- * DESCRIPTION
Size: 22.5 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago
iSEE/iSEEhex
iSEE extension for summarising data points in hexagonal bins- * DESCRIPTION
Size: 244 KB - Last synced: 6 months ago - Pushed: over 1 year ago
HelenaLC/muscat
Multi-sample multi-group scRNA-seq analysis tools- * DESCRIPTION
Size: 22.1 MB - Last synced: 20 days ago - Pushed: 9 months ago
sujit-sahu/bmstdr
This is the repository for the R package bmstdr.- * DESCRIPTION
Size: 36.5 MB - Last synced: 5 months ago - Pushed: 5 months ago
greenelab/miQC
Flexible, probablistic metrics for quality control of scRNA-seq data- * DESCRIPTION
Size: 82 KB - Last synced: 6 months ago - Pushed: over 1 year ago
jimhester/GenomicRanges 📦
- * DESCRIPTION
Size: 8.35 MB - Last synced: about 1 year ago - Pushed: about 9 years ago
vladpetyuk/celegans.aging
example of transparent and reproducible data analysis- * DESCRIPTION
Size: 142 KB - Last synced: 9 months ago - Pushed: almost 9 years ago
microbiome/mia
Microbiome analysis- * DESCRIPTION
Size: 20.8 MB - Last synced: about 15 hours ago - Pushed: about 16 hours ago
fmicompbio/monaLisa
binned motif enrichment analysis and visualisation- * DESCRIPTION
Size: 44.9 MB - Last synced: 5 days ago - Pushed: 5 days ago
j-andrews7/CRISPRball
An interactive exploration/visualization platform to help you lift the fog from your CRISPR analyses.- * DESCRIPTION
Size: 2.29 MB - Last synced: 3 days ago - Pushed: 5 months ago
stemangiola/tidySummarizedExperiment
Brings SummarizedExperiment to tidiverse with no side-effects- * DESCRIPTION
Size: 2.28 MB - Last synced: 6 days ago - Pushed: 6 days ago
lgatto/MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics- >= 2.5.19 DESCRIPTION
Size: 96.6 MB - Last synced: 3 days ago - Pushed: 5 days ago
zhangjunpeng411/miRSM
miRSM: Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information- * DESCRIPTION
Size: 3.8 MB - Last synced: 14 days ago - Pushed: about 1 month 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
rformassspectrometry/Spectra
Low level infrastructure to handle MS spectra- >= 2.5.19 DESCRIPTION
Size: 16.6 MB - Last synced: 5 days ago - Pushed: 6 days ago
tengfei/cwl.R
R objects to CWL- * DESCRIPTION
Size: 120 KB - Last synced: 22 days ago - Pushed: over 8 years ago
RajLabMSSM/echofinemap
echoverse module: Statistical and functional fine-mapping functions.- * DESCRIPTION
Size: 1.01 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
babelomics/hpAnnot
Annotation package for hiPathia- * DESCRIPTION
Size: 848 MB - Last synced: 9 months ago - Pushed: about 6 years ago
mrjc42/BiocAnnotRes2015
A repository for teaching materials I aim to use for Bioc 2015- * DESCRIPTION
Size: 394 KB - Last synced: about 1 year ago - Pushed: almost 9 years ago
waldronlab/MicrobiomeBenchmarkData
Data for benchmarking in microbiome research.- * DESCRIPTION
Size: 1.34 MB - Last synced: 3 days ago - Pushed: 4 days ago
tidyomics/plyranges
A grammar of genomic data transformation- * DESCRIPTION
Size: 3.25 MB - Last synced: 10 days ago - Pushed: 24 days ago
broadinstitute/infercnv
Inferring CNV from Single-Cell RNA-Seq- * DESCRIPTION
Size: 22.6 MB - Last synced: about 1 month ago - Pushed: 2 months ago
stemangiola/sccomp
Testing differences in cell type proportions from single-cell data.- * DESCRIPTION
Size: 88.1 MB - Last synced: 7 days ago - Pushed: 7 days ago
Bioconductor/BiocParallel
Bioconductor facilities for parallel evaluation- * DESCRIPTION
Size: 1.17 MB - Last synced: 4 days ago - Pushed: 4 days 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
esnapd/DegeneratePrimerTools 📦
Utilities for Creating and Validating Degenerate primers- >= 2.0.0 DESCRIPTION
Size: 2.05 MB - Last synced: about 1 year ago - Pushed: over 5 years ago
mountetna/monoetna
mono-repository version of etna projects- * etna/packages/magmaR/DESCRIPTION
Size: 296 MB - Last synced: 20 days ago - Pushed: 23 days ago
maize-genetics/rTASSEL
R front-end for TASSEL- * DESCRIPTION
Size: 205 MB - Last synced: 3 months ago - Pushed: 6 months ago
bhklab/PharmacoGx
R package to analyze large-scale pharmacogenomic datasets.- * DESCRIPTION
Size: 70.8 MB - Last synced: 19 days ago - Pushed: 19 days ago
insightsengineering/hermes
Preprocessing, analyzing, and reporting of RNA-seq data- * DESCRIPTION
Size: 45.2 MB - Last synced: 5 days ago - Pushed: 6 days ago
currocam/HMMERutils
A bunch of convenient functions to search for homologous sequences using the HMMER API, annotate them taxonomically, calculate physicochemical properties and facilitate exploratory analysis of homologous sequence data.- * DESCRIPTION
Size: 1.7 MB - Last synced: 10 months ago - Pushed: 10 months ago
lcolladotor/biocthis
Automate package and project setup for Bioconductor packages- * DESCRIPTION
Size: 1.24 MB - Last synced: 2 days ago - Pushed: 2 days ago
cytoscape/RCy3
New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community- * DESCRIPTION
Size: 19.4 MB - Last synced: 27 minutes ago - Pushed: about 1 month ago
npcooley/SynExtend
Tools for working with synteny objects- * DESCRIPTION
Size: 19.2 MB - Last synced: 5 days ago - Pushed: 6 days ago
MalteThodberg/BigArray
Using bigmemory as a DelayedArray Backend- * DESCRIPTION
Size: 14.6 KB - Last synced: about 1 year ago - Pushed: over 1 year ago
MalteThodberg/CAGEWorkflow
A step-by-step guide to analyzing CAGE data using R/Bioconductor- * DESCRIPTION
Size: 8.12 MB - Last synced: 7 months ago - Pushed: over 2 years ago
shenlab-sinai/geneoverlap-old
R package for testing and visualizing gene overlaps- * DESCRIPTION
Size: 1.2 MB - Last synced: about 1 month ago - Pushed: over 7 years ago
MalteThodberg/CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor- * DESCRIPTION
Size: 13.5 MB - Last synced: 10 days ago - Pushed: over 2 years ago
JEFworks-Lab/STdeconvolve
Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data- * DESCRIPTION
Size: 64.1 MB - Last synced: 6 months ago - Pushed: 6 months ago
ccb-hms/BioPlex
R-side access to PPI data from Gygi lab- * DESCRIPTION
Size: 22.4 MB - Last synced: 6 months ago - Pushed: 9 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
lgatto/ProteomicsAnnotationHubData
Annotation hub data for proteomics data- * DESCRIPTION
Size: 106 KB - Last synced: 8 months ago - Pushed: over 2 years ago
lmweber/diffcyt
R package for differential discovery analyses in high-dimensional cytometry data- * DESCRIPTION
Size: 1.52 MB - Last synced: 17 days ago - Pushed: about 2 months 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: 16 days ago - Pushed: 16 days ago
currocam/HMMERutils_old 📦
A bunch of convenient functions to search for homologous sequences using the HMMER API, annotate them taxonomically, calculate physicochemical properties and facilitate exploratory analysis of homologous sequence data.- * DESCRIPTION
Size: 4.25 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago
Oshlack/speckle
R package for specialised analysis of single cell data- * DESCRIPTION
Size: 20.4 MB - Last synced: about 1 month ago - Pushed: over 1 year ago
LieberInstitute/spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app- * DESCRIPTION
Size: 187 MB - Last synced: 2 days ago - Pushed: 2 days ago
SofieVG/FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry data- * DESCRIPTION
Size: 22 MB - Last synced: 5 months ago - Pushed: 5 months ago
griffithlab/GenVisR
Genome data visualizations- * DESCRIPTION
Size: 38 MB - Last synced: 22 days ago - Pushed: 22 days ago
dipenps/rnits
R/Bioconductor package for normalization and differential expression inference in time series gene expression microarray data- * DESCRIPTION
Size: 348 KB - Last synced: about 2 months ago - Pushed: about 1 year ago
statOmics/satuRn
satuRn is a highly performant and scalable method for performing differential transcript usage analyses.- * DESCRIPTION
Size: 6.35 MB - Last synced: 14 days ago - Pushed: about 1 year ago
genesofeve/projectR
- * DESCRIPTION
Size: 26.7 MB - Last synced: about 2 months ago - Pushed: 2 months 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
Irrationone/cellassign
Automated, probabilistic assignment of cell types in scRNA-seq data- * DESCRIPTION
Size: 14.9 MB - Last synced: 3 days ago - Pushed: over 1 year ago
cran/MetaIntegrator
:exclamation: This is a read-only mirror of the CRAN R package repository. MetaIntegrator — Meta-Analysis of Gene Expression Data. Homepage: http://biorxiv.org/content/early/2016/08/25/071514- * DESCRIPTION
Size: 4.69 MB - Last synced: 7 months ago - Pushed: 12 months 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
prostarproteomics/Prostar
- * DESCRIPTION
Size: 73.9 MB - Last synced: 23 days ago - Pushed: 23 days ago
isglobal-brge/methylclock
DNA methylation-based clocks- * DESCRIPTION
Size: 42 MB - Last synced: 24 days ago - Pushed: 5 months ago
bioFAM/MOFA2
Multi-Omics Factor Analysis- * DESCRIPTION
Size: 162 MB - Last synced: 27 days ago - Pushed: 4 months ago
Vitek-Lab/MSstatsPTM
Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments- * DESCRIPTION
Size: 21.4 MB - Last synced: 9 days ago - Pushed: 9 days ago
ctlab/phantasus
Visual exploratory analysis of gene expression data- * DESCRIPTION
Size: 48.7 MB - Last synced: 5 days ago - Pushed: 5 days ago
markrobinsonuzh/cytofWorkflow
- * DESCRIPTION
Size: 866 KB - Last synced: 18 days ago - Pushed: 18 days ago
Bioconductor/hca
Human Cell Atlas data discovery and retrieval- * DESCRIPTION
Size: 375 KB - Last synced: 3 days ago - Pushed: 4 days ago
mfansler/txcutr
R methods for generating truncated transcript annotations- * DESCRIPTION
Size: 68.4 KB - Last synced: 17 days ago - Pushed: 17 days ago
RockefellerUniversity/profileplyr
- * DESCRIPTION
Size: 9.27 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
YosefLab/VISION
Signature Analysis and Visualization for Single-Cell RNA-seq- * DESCRIPTION
Size: 94.6 MB - Last synced: 7 months ago - Pushed: about 1 year ago
tidymicrobiome/microbiomeplot
All the plot functions for tidymicrobiome- * DESCRIPTION
Size: 1.73 MB - Last synced: 9 months ago - Pushed: over 1 year ago
kasperdanielhansen/massay
- * DESCRIPTION
Size: 168 KB - Last synced: 9 months ago - Pushed: almost 9 years ago
Bioconductor/biocViews
Categorized views of R package repositories- * DESCRIPTION
Size: 1.47 MB - Last synced: 3 days ago - Pushed: 4 days ago
rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data- * DESCRIPTION
Size: 20.9 MB - Last synced: 20 days ago - Pushed: 21 days ago
saraovetto/SmithWaterman
R package that performs local sequence alignment of two nucleic acid sequences according to the Smith Waterman greedy algorithm.- * SmithWaterman package/DESCRIPTION
Size: 360 KB - Last synced: 10 months ago - Pushed: over 1 year ago
Rafael-Ayala/asteRisk
astrodynamics in R- * DESCRIPTION
Size: 80.9 MB - Last synced: 21 days ago - Pushed: about 2 months ago
mtmorgan/cellxgenedp
R interface to the cellxgene data portal- * DESCRIPTION
Size: 6.96 MB - Last synced: 3 days ago - Pushed: about 1 month ago
HelenLindsay/AbNames
Standardize antibody names and match to genes- * DESCRIPTION
Size: 42.1 MB - Last synced: 11 months ago - Pushed: 11 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/JSB-UCLA/scPNMF/DESCRIPTION
- * _repos/github/NathanSkene/EWCE/DESCRIPTION
- * _repos/github/NathanSkene/MAGMA_Celltyping/DESCRIPTION
- * _repos/github/RajLabMSSM/echolocatoR/DESCRIPTION
- * _repos/github/SofieVG/FlowSOM/DESCRIPTION
- * _repos/github/haoharryfeng/NeuCA/DESCRIPTION
- * _repos/github/kendomaniac/docker4seq/DESCRIPTION
- * _repos/github/kendomaniac/rCASC/DESCRIPTION
- * _repos/github/radio1988/OneStopRNAseq/DESCRIPTION
Size: 433 MB - Last synced: 3 days ago - Pushed: 5 days ago
epiviz/epivizrStandalone
Run all epiviz components locally- * DESCRIPTION
Size: 56.6 KB - Last synced: 26 days ago - Pushed: about 3 years ago
rnabioco/someta
Inclusion of processed cell metadata improves single cell sequencing analysis reproducibility and accessibility- * DESCRIPTION
Size: 339 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago
dtm2451/dittoSeq
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data- * DESCRIPTION
Size: 18.7 MB - Last synced: 5 days ago - Pushed: 5 days ago
camilleroquencourt/ptairMS
- * DESCRIPTION
Size: 17.2 MB - Last synced: 2 days ago - Pushed: 12 days ago
amcdavid/CellaRepertorium
Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)- * DESCRIPTION
Size: 16.3 MB - Last synced: 15 days ago - Pushed: almost 2 years ago
computational-metabolomics/msPurity
R-package - Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics- * DESCRIPTION
Size: 12.8 MB - Last synced: 9 days ago - Pushed: 8 months ago
prostarproteomics/DaparViz
- * DESCRIPTION
Size: 8.94 MB - Last synced: 2 months ago - Pushed: 2 months ago
waldronlab/curatedTCGAData
Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects- * DESCRIPTION
Size: 2.26 MB - Last synced: 3 days ago - Pushed: 4 days 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: 4 days ago