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.
  ☆57Updated last year
• Vivianstats / scLink
  Inferring gene co-expression networks from single cell gene expression data
  ☆28Updated 3 years ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆57Updated last year
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆57Updated 4 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
• sigven / oncoEnrichR
  Explore the cancer relevance of your gene list
  ☆52Updated 2 weeks ago
• saezlab / transcriptutorial
  This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
  ☆56Updated 2 years ago
• icbi-lab / Immunophenogram
  ☆41Updated 7 years ago
• inutano / chip-atlas
  ChIP-Atlas: Browse and analyze all public ChIP/DNase-seq data on your browser
  ☆78Updated last week
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆28Updated 2 years ago
• YosefLab / ImpulseDE2
  ☆39Updated 3 years ago
• slowkow / tftargets
  Human transcription factor target genes from 6 databases in convenient R format.
  ☆86Updated 7 years ago
• waldronlab / HGNChelper
  Identify and correct invalid gene symbols
  ☆59Updated 10 months ago
• GreenleafLab / motifmatchr
  Fast motif matching in R
  ☆46Updated last year
• antigenomics / vdjmatch
  ⚙️ Matching T-cell repertoire against a database of TCR antigen specificities
  ☆39Updated 6 years ago
• cole-trapnell-lab / cicero-release
  ☆58Updated last year
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆78Updated 6 months ago
• shenorrLabTRDF / bseqsc
  Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
  ☆46Updated 2 years ago
• hemberg-lab / scfind
  ☆43Updated last year
• broadinstitute / single_cell_portal_core
  Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
  ☆68Updated this week
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆55Updated 4 years ago
• fpbarthel / GLASS
  GLASS consortium
  ☆42Updated 5 years ago
• fmicompbio / monaLisa
  binned motif enrichment analysis and visualisation
  ☆41Updated 2 weeks ago
• pachterlab / kallisto-transcriptome-indices
  Reference transcriptome indices build from kallisto for popular organisms
  ☆43Updated last year
• satijalab / azimuth-references
  ☆24Updated 4 months ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• PierreBSC / Viral-Track
  ☆62Updated 5 years ago
• almeidasilvaf / BioNERO
  Easy and comprehensive biological network reconstruction and analysis
  ☆32Updated 2 weeks ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆46Updated last year