Alternatives and similar repositories for ALLCools

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

• zhoujt1994 / scHiCluster
  ☆69Updated last month
• HYsxe / PRINT
  ☆37Updated last year
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆30Updated 2 months ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated 11 months ago
• lhqing / cemba_data
  Mapping pipeline for snmC-seq based technologies.
  ☆20Updated 2 years ago
• rajewsky-lab / spacemake
  ☆48Updated last week
• UPSUTER / GEMLI
  ☆32Updated 11 months ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆24Updated last year
• dpeerlab / Harmony
  Harmony framework for connecting scRNA-seq data from discrete time points
  ☆53Updated last month
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆67Updated 5 months ago
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆30Updated last week
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆32Updated 2 years ago
• HuMingLab / SnapHiC
  SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data
  ☆42Updated 2 years ago
• DeplanckeLab / ChromatinHD
  High-definition modeling of chromatin + transcriptomics data
  ☆26Updated 8 months ago
• Teichlab / snp2cell
  cell type specific, trait-associated gene regulation
  ☆29Updated 9 months ago
• doraadong / TraSig
  Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
  ☆25Updated 2 years ago
• wenweixiong / MARVEL
  ☆53Updated last year
• yal054 / epiformer
  ☆26Updated 8 months ago
• josephreplogle / guide_calling
  Tools for sgRNA calling in direct capture Perturb-seq data
  ☆39Updated 2 years ago
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆19Updated 4 years ago
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated last year
• aertslab / scATAC-seq_benchmark
  ☆19Updated 2 years ago
• atarashansky / SAMap
  SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
  ☆85Updated last week
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆33Updated 3 weeks ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆58Updated 4 years ago
• swaruplabUCI / ArchRtoSignac
  An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
  ☆37Updated last year
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 3 years ago
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆32Updated 2 years ago
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆43Updated 3 weeks ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆43Updated 2 years ago