Alternatives and similar repositories for MOFA

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

• dviraran / xCell
  Cell types enrichment analysis
  ☆197Updated last year
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆149Updated 2 years ago
• YeoLab / single-cell-bioinformatics
  Course material in notebook format for learning about single cell bioinformatics methods
  ☆102Updated 8 years ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆287Updated 3 weeks ago
• mskcc / RNAseqDB
  ☆141Updated 7 years ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆193Updated 2 years ago
• hms-dbmi / scde
  R package for analyzing single-cell RNA-seq data
  ☆175Updated last year
• zhangyuqing / ComBat-seq
  Batch effect adjustment based on negative binomial regression for RNA sequencing count data
  ☆179Updated 4 years ago
• bioFAM / MOFA2
  Multi-Omics Factor Analysis
  ☆336Updated 11 months ago
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆126Updated last year
• Oshlack / splatter
  Simple simulation of single-cell RNA sequencing data
  ☆226Updated last week
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆174Updated 10 months ago
• alserglab / fgsea
  Fast Gene Set Enrichment Analysis
  ☆401Updated 2 weeks ago
• stephenturner / annotables
  R data package for annotating/converting Gene IDs
  ☆163Updated 2 years ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆182Updated 3 weeks ago
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆241Updated last year
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆216Updated last year
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆324Updated this week
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆191Updated last week
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• kevinblighe / E-MTAB-6141
  Data from Lewis, Barnes, Blighe et al., Cell Rep. 2019 Aug 27; 28(9): 2455–2470.e5.
  ☆121Updated 5 years ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆283Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆148Updated last year
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• HelenaLC / muscat
  Multi-sample multi-group scRNA-seq analysis tools
  ☆193Updated 3 weeks ago
• csoneson / conquer_comparison
  Code for evaluation of differential expression methods in single-cell RNA-seq data
  ☆112Updated 4 years ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆413Updated last month
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆369Updated last week
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆283Updated 2 years ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆309Updated 4 years ago