Alternatives and similar repositories for ALLCools:

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

• zhoujt1994 / scHiCluster
  ☆63Updated 2 months ago
• lhqing / cemba_data
  Mapping pipeline for snmC-seq based technologies.
  ☆19Updated last year
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated 11 months ago
• wenweixiong / MARVEL
  ☆46Updated 8 months ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆39Updated 2 months ago
• HYsxe / PRINT
  ☆36Updated 6 months ago
• qinqian / lisa
  epigenome analysis to rank transcription factors
  ☆30Updated 2 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆44Updated 4 years ago
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 2 years ago
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆41Updated 8 months ago
• UPSUTER / GEMLI
  ☆30Updated 2 months ago
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated last year
• cole-trapnell-lab / cicero-release
  ☆59Updated 7 months ago
• liulab-dfci / lisa2
  ☆30Updated 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…
  ☆19Updated 9 months ago
• aertslab / create_cisTarget_databases
  Create cisTarget databases
  ☆47Updated last month
• dbrg77 / scATAC_snakemake
  Snakemake pipeline for plate scATAC-seq processing
  ☆26Updated last year
• tanlabcode / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆24Updated 6 months ago
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆26Updated 3 years ago
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆15Updated 3 years ago
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated 3 months ago
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆22Updated 4 months ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆45Updated last year
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆48Updated 8 months ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆58Updated 2 years ago
• BIMSBbioinfo / ikarus
  Identifying tumor cells at the single-cell level using machine learning
  ☆47Updated 4 months ago
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆41Updated last year
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆23Updated last week
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆29Updated 2 weeks ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆47Updated 3 years ago