Alternatives and similar repositories for ALLCools

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

• zhoujt1994 / scHiCluster
  ☆68Updated 4 months ago
• dpeerlab / Harmony
  Harmony framework for connecting scRNA-seq data from discrete time points
  ☆51Updated last year
• HYsxe / PRINT
  ☆36Updated last year
• lhqing / cemba_data
  Mapping pipeline for snmC-seq based technologies.
  ☆21Updated 2 years ago
• UPSUTER / GEMLI
  ☆32Updated 8 months ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated 8 months ago
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆30Updated 2 years ago
• wenweixiong / MARVEL
  ☆51Updated last year
• juliaolivieri / SpliZ_pipeline
  Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis
  ☆34Updated 3 years ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆22Updated last year
• cbg-ethz / SCICoNE
  Single-cell copy number calling and event history reconstruction.
  ☆27Updated 9 months ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆46Updated last year
• HuMingLab / SnapHiC
  SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data
  ☆41Updated 2 years ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆57Updated 4 years ago
• liulab-dfci / lisa2
  ☆30Updated 2 years ago
• lcmmichielsen / scHPL
  ☆37Updated 7 months ago
• tanlabcode / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆24Updated last year
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆34Updated 3 months ago
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆29Updated 3 weeks ago
• DeplanckeLab / ChromatinHD
  High-definition modeling of chromatin + transcriptomics data
  ☆25Updated 5 months ago
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆54Updated 3 years ago
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated 9 months ago
• cole-trapnell-lab / cicero-release
  ☆58Updated last year
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆18Updated 3 years ago
• dbrg77 / scATAC_snakemake
  Snakemake pipeline for plate scATAC-seq processing
  ☆26Updated last year
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated 2 years ago
• gxiaolab / scAllele
  ☆38Updated last month
• Xinglab / PEGASAS
  Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)
  ☆20Updated 3 years ago
• mcvickerlab / varCA
  Use an ensemble of variant callers to call variants from ATAC-seq data
  ☆23Updated 4 months ago
• gwlab-ca / scsnv
  scSNV Mapping tool for 10X Single Cell Data
  ☆25Updated last year