Alternatives and similar repositories for recount3

Users that are interested in recount3 are comparing it to the libraries listed below

• combiz / scFlow
  Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
  ☆56Updated last year
• saezlab / transcriptutorial
  This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
  ☆55Updated 2 years ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆57Updated 9 months ago
• sigven / oncoEnrichR
  Explore the cancer relevance of your gene list
  ☆51Updated 4 months ago
• hukai916 / scATACpipe
  ☆27Updated 8 months ago
• waldronlab / HGNChelper
  Identify and correct invalid gene symbols
  ☆58Updated 7 months ago
• antigenomics / vdjmatch
  ⚙️ Matching T-cell repertoire against a database of TCR antigen specificities
  ☆38Updated 6 years ago
• slowkow / tftargets
  Human transcription factor target genes from 6 databases in convenient R format.
  ☆86Updated 6 years ago
• GreenleafLab / motifmatchr
  Fast motif matching in R
  ☆47Updated last year
• Vivianstats / scLink
  Inferring gene co-expression networks from single cell gene expression data
  ☆24Updated 2 years ago
• broadinstitute / single_cell_portal_core
  Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
  ☆68Updated last week
• pachterlab / kallisto-transcriptome-indices
  Reference transcriptome indices build from kallisto for popular organisms
  ☆42Updated last year
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆30Updated 3 years ago
• Nik-Zainal-Group / signature.tools.lib
  R package containing useful functions for mutational signature analysis
  ☆82Updated last week
• PierreBSC / Viral-Track
  ☆57Updated 4 years ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆45Updated last year
• broadinstitute / RNA_MUTECT_1.0-1
  ☆38Updated 5 years ago
• icbi-lab / immune_deconvolution_benchmark
  Reproducible pipeline for "Comprehensive evaluation of cell-type quantification methods for immuno-oncology", Sturm et al. 2019, https://…
  ☆43Updated 5 years ago
• fmicompbio / monaLisa
  binned motif enrichment analysis and visualisation
  ☆40Updated last week
• qinqian / lisa
  epigenome analysis to rank transcription factors
  ☆30Updated 2 years ago
• HumanCellAtlas / skylab
  Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
  ☆48Updated 4 months ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• reimandlab / ActivePathways
  Integrative pathway enrichment analysis of multivariate omics data
  ☆112Updated 2 weeks ago
• shenorrLabTRDF / bseqsc
  Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
  ☆45Updated 2 years ago
• montilab / hypeR
  An R Package for Geneset Enrichment Workflows
  ☆76Updated last month
• nf-core / scflow
  Please consider using/contributing to https://github.com/nf-core/scdownstream
  ☆25Updated last year
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆76Updated 4 months ago
• fpbarthel / GLASS
  GLASS consortium
  ☆39Updated 5 years ago
• YosefLab / ImpulseDE2
  ☆38Updated 2 years ago
• wgmao / PLIER
  Pathway-Level Information Extractor (PLIER): a generative model for gene expression data
  ☆54Updated 10 months ago