Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: bioconductor
rformassspectrometry/Spectra
Low level infrastructure to handle MS spectra
Language: R - Size: 19.2 MB - Last synced: about 12 hours ago - Pushed: about 13 hours ago - Stars: 31 - Forks: 23
stemangiola/tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
Language: R - Size: 95.1 MB - Last synced: about 20 hours ago - Pushed: about 20 hours ago - Stars: 159 - Forks: 23
Bioconductor/bioconductor.org
Source code for the Bioconductor website
Language: HTML - Size: 82.3 MB - Last synced: about 16 hours ago - Pushed: 1 day ago - Stars: 23 - Forks: 42
LieberInstitute/spatialDLPFC
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
Language: HTML - Size: 14.9 GB - Last synced: about 18 hours ago - Pushed: 1 day ago - Stars: 10 - Forks: 0
stemangiola/tidySingleCellExperiment
Brings SingleCellExperiment objects to the tidyverse
Language: R - Size: 41.2 MB - Last synced: about 7 hours ago - Pushed: 1 day ago - Stars: 34 - Forks: 7
carpentries-incubator/bioc-project
Introduction to the Bioconductor project
Language: R - Size: 11.6 MB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 17 - Forks: 15
Appsilon/shiny.gosling
R Shiny wrapper for Gosling.js - Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization
Language: R - Size: 13.7 MB - Last synced: about 22 hours ago - Pushed: 1 day ago - Stars: 16 - Forks: 1
lgatto/MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
Language: R - Size: 96.9 MB - Last synced: about 21 hours ago - Pushed: 1 day ago - Stars: 120 - Forks: 50
grimbough/biomaRt
R package providing query functionality to BioMart instances like Ensembl
Language: R - Size: 2.22 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 31 - Forks: 13
lcolladotor/cshl_rstats_genome_scale_2024
CSHL Statistical Analysis of Genome Scale Data 2024
Language: R - Size: 20.3 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 1 - Forks: 0
rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data
Language: R - Size: 21.4 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 21 - Forks: 6
theislab/anndata2ri
Convert between AnnData and SingleCellExperiment
Language: Python - Size: 178 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 114 - Forks: 16
ccb-hms/osca-workbench
Single-cell RNAseq materials derived from the 2023 ISMB OSCA workshop in the carpentries workbench format.
Language: R - Size: 879 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0
carpentries-incubator/bioc-intro
Bioconductor data science introduction
Language: R - Size: 730 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 28 - Forks: 27
charles-plessy/CAGEr
Mirror of Bioconductor's CAGEr package repository
Language: HTML - Size: 6.92 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 6 - Forks: 4
lpantano/DEGreport
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
Language: R - Size: 51.7 MB - Last synced: 3 days ago - Pushed: 3 months ago - Stars: 22 - Forks: 16
mikelove/alpine
Modeling and correcting fragment sequence bias for RNA-seq
Language: R - Size: 1.28 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 24 - Forks: 5
Boehringer-Ingelheim/Personalis-io
Read Personalis datasets into MultiAssayExperiment objects
Language: R - Size: 19.6 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0
microbiome/mia
Microbiome analysis
Language: R - Size: 20.6 MB - Last synced: about 2 hours ago - Pushed: about 3 hours ago - Stars: 43 - Forks: 23
schifferl/tuberculosis
Tuberculosis Gene Expression Data for Machine Learning
Language: R - Size: 84 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 2 - Forks: 0
schifferl/MultimodalExperiment
Integrative Bulk and Single-Cell Experiment Container
Language: R - Size: 2.91 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0
vjcitn/SCecosys
Discuss data/software ecosystem for single cell genomics
Size: 696 KB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
vjcitn/BiocRJournal
contributions to R Journal
Language: HTML - Size: 149 KB - Last synced: 6 days ago - Pushed: 6 months ago - Stars: 0 - Forks: 1
vjcitn/YESCDS2
Updating YESCDS with webr
Language: JavaScript - Size: 438 KB - Last synced: 6 days ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0
vjcitn/BiocHail
Using hail via Basilisk
Language: R - Size: 18 MB - Last synced: 6 days ago - Pushed: 12 months ago - Stars: 6 - Forks: 0
nanxstats/Rcpi
💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery
Language: R - Size: 10.3 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 35 - Forks: 12
Bioconductor/bioconductor_docker
Docker Containers for Bioconductor - NEW!
Language: Shell - Size: 288 KB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 70 - Forks: 30
MoseleyBioinformaticsLab/categoryCompare2
Enables Gene Ontology (and other feature annotation) enrichment calculations and comparisons between feature sets.
Language: R - Size: 32.1 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 1 - Forks: 1
Bioconductor/BiocStickers
Stickers for some Bioconductor packages - feel free to contribute and/or modify.
Language: R - Size: 360 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 117 - Forks: 86
iSEE/iSEEWorkshopEuroBioc2020
Workshop on interactive analysis of SummarizedExperiment objects with iSEE for EuroBioc2020
Language: CSS - Size: 24.9 MB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1
iSEE/iSEEhex
iSEE extension for summarising data points in hexagonal bins
Language: R - Size: 244 KB - Last synced: 7 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
Genometric/TVQ
Contains scripts to study the impact of publishing software to package management systems on their scholarly recognition.
Language: C# - Size: 3.85 MB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1
LieberInstitute/spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app
Language: R - Size: 187 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 72 - Forks: 15
almeidasilvaf/cogeqc_paper
Data and code associated with the paper "Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package"
Language: TeX - Size: 79.9 MB - Last synced: 7 days ago - Pushed: 7 months ago - Stars: 1 - Forks: 1
Bioconductor/bioc_git_transition
This python package is for transitioning bioconductor from SVN to git
Language: Python - Size: 2.94 MB - Last synced: 8 days ago - Pushed: about 1 year ago - Stars: 14 - Forks: 1
Bioconductor/Contributions
Contribute Packages to Bioconductor
Size: 46.9 KB - Last synced: 8 days ago - Pushed: 8 months ago - Stars: 131 - Forks: 33
UCLouvain-CBIO/CTexploreR
Explores Cancer Testis Genes
Language: R - Size: 17.6 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0
neurogenomics/rworkflows
Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.
Language: HTML - Size: 12.6 MB - Last synced: 7 days ago - Pushed: 4 months ago - Stars: 66 - Forks: 6
LieberInstitute/Visium_SPG_AD
Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.
Language: HTML - Size: 2.09 GB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 1 - Forks: 0
benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
Language: R - Size: 467 MB - Last synced: 8 days ago - Pushed: 4 months ago - Stars: 453 - Forks: 141
elsayed-lab/hpgltools
A collection of R functions to aid in host-pathogen genomic research
Language: R - Size: 555 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 10 - Forks: 8
Bioconductor/GenomicDataCommons
Provide R access to the NCI Genomic Data Commons portal.
Language: R - Size: 4.38 MB - Last synced: 8 days ago - Pushed: 10 days ago - Stars: 82 - Forks: 23
bernatgel/karyoploteR
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
Language: R - Size: 3.06 MB - Last synced: 8 days ago - Pushed: 4 months ago - Stars: 287 - Forks: 40
theislab/zellkonverter
Conversion between scRNA-seq objects
Language: R - Size: 1.6 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 132 - Forks: 26
r-hub/biocatgh
Bioconductor code mirror ar https://github.com/bioc
Language: R - Size: 47.9 KB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0
acinostroza/TargetSearchData
Example GC-MS data for TargetSearch Package
Language: TeX - Size: 29.1 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 1 - Forks: 1
acinostroza/TargetSearch
R package for the analysis of GC-MS metabolite profiling data. This git repository mirrors the TargetSearch git repository on bioconductor.
Language: R - Size: 993 KB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 4 - Forks: 0
mikelove/bioc-refcard
Bioconductor cheat sheet
Language: R - Size: 65.4 KB - Last synced: 8 days ago - Pushed: about 2 years ago - Stars: 182 - Forks: 64
lcolladotor/bioc_team_ds
R/Bioconductor-powered Team Data Science by Leonardo Collado Torres
Language: HTML - Size: 3.62 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 2 - Forks: 3
LieberInstitute/TREG
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Language: R - Size: 22.7 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 4 - Forks: 2
LieberInstitute/qsvaR
Quality Surrogate Variable Analysis for Degradation Correction
Language: R - Size: 7.68 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 2
LieberInstitute/brainflowprobes
A package to annotate and visualize expression of candidate BrainFlow probe sequences.
Language: R - Size: 15.9 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 1 - Forks: 0
lcolladotor/biocthis
Automate package and project setup for Bioconductor packages
Language: R - Size: 1.24 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 49 - Forks: 16
LieberInstitute/recountWorkflow
Public repo for the recount Bioconductor workflow that is visible at http://bioconductor.org/help/workflows/
Language: TeX - Size: 1.59 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 4 - Forks: 0
LieberInstitute/recount3
Explore and download data from the recount3 project
Language: R - Size: 2.7 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 27 - Forks: 4
leekgroup/recount
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
Language: R - Size: 40.8 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 40 - Forks: 9
leekgroup/derfinderPlot
Plotting functions for derfinder results
Language: R - Size: 17.3 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 2 - Forks: 0
leekgroup/derfinderHelper
Helper package for derfinder
Language: R - Size: 371 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0
leekgroup/derfinderData
Example data used by the derfinder and derfinderData Bioconductor packages
Language: R - Size: 30.6 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0
lcolladotor/derfinder
Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
Language: R - Size: 11.5 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 42 - Forks: 15
microbiome/miaViz
Microbiome Analysis Plotting and Visualization
Language: R - Size: 1.24 GB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 7 - Forks: 8
LieberInstitute/DeconvoBuddies
Helper Functions for LIBD Deconvolution
Language: R - Size: 47.3 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 2 - Forks: 1
Bioconductor/bioconductor_salt
Salt to configure Linux and Mac (x86_64, arm64) for the BBS
Language: SaltStack - Size: 242 KB - Last synced: 8 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 3
iSEE/iSEEhub
Custom landing page for iSEE and the Bioconductor ExperimentHub
Language: R - Size: 6.15 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 4 - Forks: 0
iSEE/iSEEde
iSEE extension for panels related to differential expression analysis
Language: R - Size: 3.36 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 1
federicomarini/GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
Language: R - Size: 115 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 75 - Forks: 8
federicomarini/HCAData
Access data from the Human Cell Atlas project, directly via R/Bioconductor
Language: R - Size: 7.37 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 8 - Forks: 2
federicomarini/ideal
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
Language: R - Size: 24 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 29 - Forks: 7
federicomarini/pcaExplorer
pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data
Language: R - Size: 57.4 MB - Last synced: 5 days ago - Pushed: 14 days ago - Stars: 52 - Forks: 17
federicomarini/flowcatchR
A framework for tracking and analyzing flowing blood cells in time lapse microscopy images
Language: R - Size: 24.8 MB - Last synced: 7 days ago - Pushed: 14 days ago - Stars: 5 - Forks: 0
waldronlab/MultiAssayExperiment
Bioconductor package for management of multi-assay data
Language: R - Size: 6.86 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 68 - Forks: 32
waldronlab/HMP16SData
16S rRNA Sequencing Data from the Human Microbiome Project
Language: R - Size: 46.6 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 9 - Forks: 5
waldronlab/curatedMetagenomicData
Curated Metagenomic Data of the Human Microbiome
Language: R - Size: 176 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 119 - Forks: 27
BioinformaticsFMRP/TCGAbiolinks
TCGAbiolinks
Language: R - Size: 349 MB - Last synced: 6 days ago - Pushed: about 1 month ago - Stars: 275 - Forks: 107
aoles/RBioFormats
:books: R interface to the Bio-Formats library
Language: R - Size: 118 MB - Last synced: 14 days ago - Pushed: 16 days ago - Stars: 23 - Forks: 13
mhahsler/rBLAST
Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
Language: R - Size: 450 KB - Last synced: 14 days ago - Pushed: 16 days ago - Stars: 100 - Forks: 22
lpantano/isomiRs
analyze isomiRs from seqbuster tool
Language: R - Size: 28.6 MB - Last synced: 3 days ago - Pushed: 13 days ago - Stars: 8 - Forks: 3
UCLouvain-CBIO/LSTAT2340
Traitement statistique de données omiques
Language: HTML - Size: 21.9 MB - Last synced: 7 days ago - Pushed: 18 days ago - Stars: 0 - Forks: 0
mhahsler/rRDP
Seamlessly interfaces RDP classifier.
Language: R - Size: 2.86 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 1 - Forks: 1
Bioconductor/bioc_coc_multilingual
Multilingual version of the Bioconductor Code of Conduct
Language: CSS - Size: 1.34 MB - Last synced: 8 days ago - Pushed: 20 days ago - Stars: 1 - Forks: 15
BiodataAnalysisGroup/tripr
T-cell Receptor/Immunoglobulin Profiler {tripr}
Language: R - Size: 10 MB - Last synced: 2 days ago - Pushed: 21 days ago - Stars: 2 - Forks: 4
LTLA/scRNAseq
Clone of the Bioconductor repository for the scRNAseq package.
Language: R - Size: 50.1 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 22 - Forks: 12
tidyomics/plyranges
A grammar of genomic data transformation
Language: R - Size: 3.25 MB - Last synced: 21 days ago - Pushed: about 1 month ago - Stars: 134 - Forks: 19
seandavi/BiocPkgTools
Computable build reports, package metadata, and download stats from the Bioconductor project
Language: R - Size: 5.14 MB - Last synced: 15 days ago - Pushed: 21 days ago - Stars: 19 - Forks: 10
lcolladotor/DSgs_logs
Data Science guidance session logs
Language: HTML - Size: 4.87 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 0 - Forks: 0
neurogenomics/EpiCompare
Comparison, benchmarking & QC of epigenetic datasets
Language: HTML - Size: 29.7 MB - Last synced: 7 days ago - Pushed: 21 days ago - Stars: 12 - Forks: 3
BodenmillerGroup/cytoviewer
An interactive multi-channel image viewer for R
Language: R - Size: 4.99 MB - Last synced: 21 days ago - Pushed: 4 months ago - Stars: 5 - Forks: 1
grimbough/bioc-actions
GitHub Actions for developing and maintaining Bioconductor packages
Language: R - Size: 127 KB - Last synced: 7 days ago - Pushed: 16 days ago - Stars: 9 - Forks: 3
MicrobialGenomics-IrsicaixaOrg/dar
dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.
Language: R - Size: 38.5 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0
ropensci/BaseSet
Provides classes for working with sets
Language: R - Size: 7.36 MB - Last synced: 5 days ago - Pushed: 3 months ago - Stars: 10 - Forks: 3
Oshlack/splatter
Simple simulation of single-cell RNA sequencing data
Language: R - Size: 57.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 205 - Forks: 55
seandavi/GEOquery
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
Language: R - Size: 19.1 MB - Last synced: 1 day ago - Pushed: 6 months ago - Stars: 82 - Forks: 34
pachterlab/voyager
From geospatial to spatial -omics
Language: R - Size: 4.1 GB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 60 - Forks: 6
rmflight/categoryCompare
Github repo of the categoryCompare meta-analysis package
Language: R - Size: 8.2 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 5 - Forks: 0
CarlosUziel/goi-strat
GoiStrat - A novel supervised approach to gene of interest based sample stratification and analysis to assess biological differences
Language: Python - Size: 6.72 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0
datacamp/rdocumentation-2.0
📚 RDocumentation provides an easy way to search the documentation for every version of every R package on CRAN and Bioconductor.
Language: TypeScript - Size: 829 KB - Last synced: 24 days ago - Pushed: 25 days ago - Stars: 265 - Forks: 43
rformassspectrometry/MsCoreUtils
Core Utils for Mass Spectrometry Data
Language: R - Size: 12.5 MB - Last synced: 7 days ago - Pushed: 25 days ago - Stars: 16 - Forks: 11
MicTott/SpotSweeper
Spatially-aware quality control for spatial transcriptomics
Language: R - Size: 27.8 MB - Last synced: 14 days ago - Pushed: 27 days ago - Stars: 0 - Forks: 0
crisprVerse/crisprScore
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
Language: Python - Size: 80.7 MB - Last synced: 8 days ago - Pushed: about 2 months ago - Stars: 9 - Forks: 2
UCLouvain-CBIO/depmap
Cancer Dependency Map package
Language: R - Size: 1.48 GB - Last synced: 7 days ago - Pushed: about 2 months ago - Stars: 24 - Forks: 7