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

smped/ngsReports
  • * DESCRIPTION

Size: 38.1 MB - Last synced: 1 day ago - Pushed: 1 day 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

SydneyBioX/simpleSeg
  • * DESCRIPTION

Size: 104 MB - Last synced: 26 days ago - Pushed: 26 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

microbiome/miaTime
  • * DESCRIPTION

Size: 5.09 MB - Last synced: 11 days ago - Pushed: 11 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