Alternatives and similar repositories for epiformer

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

• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated 6 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆63Updated 3 weeks ago
• jcao89757 / TESSA
  Mapping the Functional Landscape of TCR Repertoire
  ☆34Updated 3 years ago
• zhoujt1994 / scHiCluster
  ☆67Updated 2 months ago
• josephreplogle / guide_calling
  Tools for sgRNA calling in direct capture Perturb-seq data
  ☆36Updated 2 years ago
• wanglabtongji / SCRIP
  SCRIP(Single Cell Regulatory network Inference using ChIP-seq) is a tool for evaluating the binding enrichment of specific TR at single-c…
  ☆20Updated last year
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆18Updated 3 years ago
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆33Updated last month
• wenweixiong / MARVEL
  ☆49Updated last year
• HYsxe / PRINT
  ☆35Updated 10 months ago
• xmuhuanglab / eNet
  ☆12Updated 2 years ago
• aertslab / CREsted
  CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…
  ☆43Updated this week
• Teichlab / snp2cell
  cell type specific, trait-associated gene regulation
  ☆27Updated 4 months ago
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆26Updated this week
• FunctionLab / sei-manuscript
  Code for reproducing the Sei manuscript results
  ☆17Updated 3 years ago
• beyondpie / CEMBA_wmb_snATAC
  Whole mouse brain snATAC seq analysis
  ☆27Updated 3 months ago
• dbrg77 / scATAC_snakemake
  Snakemake pipeline for plate scATAC-seq processing
  ☆26Updated last year
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆70Updated last week
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆43Updated last year
• SUwonglab / PECA
  PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
  ☆44Updated last year
• satijalab / PASTA
  ☆20Updated 11 months ago
• DeplanckeLab / ChromatinHD
  High-definition modeling of chromatin + transcriptomics data
  ☆24Updated 3 months ago
• aertslab / ScoMAP
  ScoMAP is an R package to spatially integrate single-cell omics data into virtual cells and infer enhancer-to-gene relationships.
  ☆27Updated 3 years ago
• Papatheodorou-Group / BENGAL
  Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
  ☆39Updated 2 weeks ago
• SchulzLab / STARE
  TF analysis from epigenetic and Hi-C data
  ☆17Updated 4 months ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆19Updated last year
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 2 years ago
• inmybrain / SClineager
  SClineager: a Bayesian hierarchical model that performs lineage tracing of single cells based on genetic markers
  ☆10Updated last year
• liulab-dfci / lisa2
  ☆30Updated 2 years ago
• UPSUTER / GEMLI
  ☆32Updated 6 months ago