Alternatives and similar repositories for MOFA

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

• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆195Updated 2 years ago
• dviraran / xCell
  Cell types enrichment analysis
  ☆206Updated last year
• mskcc / RNAseqDB
  ☆143Updated 7 years ago
• Oshlack / splatter
  Simple simulation of single-cell RNA sequencing data
  ☆233Updated last week
• zhangyuqing / ComBat-seq
  Batch effect adjustment based on negative binomial regression for RNA sequencing count data
  ☆201Updated 5 years ago
• hemberg-lab / scRNA.seq.datasets
  Collection of public scRNA-Seq datasets used by our group
  ☆174Updated 4 years ago
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆148Updated 3 years ago
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆190Updated 3 years ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆308Updated 3 months ago
• Irrationone / cellassign
  Automated, probabilistic assignment of cell types in scRNA-seq data
  ☆210Updated 3 years ago
• hms-dbmi / scde
  R package for analyzing single-cell RNA-seq data
  ☆179Updated last year
• bioFAM / MOFA2
  Multi-Omics Factor Analysis
  ☆371Updated last week
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆217Updated last year
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆299Updated 2 years ago
• YeoLab / single-cell-bioinformatics
  Course material in notebook format for learning about single cell bioinformatics methods
  ☆100Updated 9 years ago
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆143Updated last year
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆246Updated 6 months ago
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆218Updated 2 years ago
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Updated last year
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆257Updated 3 months ago
• Olink-Proteomics / OlinkRPackage
  Olink R package: A collection of functions to facilitate analysis of proteomic data from Olink. The goal of this package is to help users…
  ☆124Updated this week
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆185Updated this week
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆185Updated last year
• stephenturner / annotables
  R data package for annotating/converting Gene IDs
  ☆168Updated 6 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆288Updated last year
• hemberg-lab / SC3
  A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
  ☆129Updated 4 years ago
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆230Updated 3 years ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆292Updated 6 months ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 5 years ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆119Updated 3 years ago