Alternatives and similar repositories for toolkit

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

• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆60Updated last month
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• natsuhiko / rasqual
  Robust Allele Specific Quantification and quality controL
  ☆40Updated 3 years ago
• qinqian / lisa
  epigenome analysis to rank transcription factors
  ☆31Updated 2 years ago
• nghiavtr / SCmut
  ☆34Updated 6 years ago
• BuysDB / SingleCellMultiOmics
  Tools which deal with multiple single cell measurements
  ☆24Updated 3 months 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
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆113Updated 2 weeks ago
• cole-trapnell-lab / cicero-release
  ☆59Updated last year
• cbg-ethz / SCICoNE
  Single-cell copy number calling and event history reconstruction.
  ☆27Updated 10 months ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• lcmmichielsen / scHPL
  ☆37Updated 8 months ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆77Updated 2 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated 2 years ago
• dphansti / mango
  chia pet analysis software
  ☆25Updated 6 years ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• yjzhang / split-seq-pipeline
  ☆22Updated 5 years ago
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆55Updated 4 years ago
• UcarLab / AMULET
  A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.
  ☆31Updated 2 years ago
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆54Updated 4 years ago
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆32Updated 3 years ago
• WeiqiangZhou / BIRD
  Big data Regression for predicting DNase I hypersensitivity
  ☆31Updated last year
• vierstralab / motif-clustering
  Clustering motif models to remove redundancy
  ☆43Updated 2 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆60Updated 4 years ago
• YeoLab / singlecell_pnm
  Code and figures accompanying the paper, "Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neu…
  ☆20Updated 8 years ago
• BUStools / bustools
  Tools for working with BUS files
  ☆102Updated 5 months ago
• HorvathLab / NGS
  Next-Gen Sequencing tools from the Horvath Lab
  ☆44Updated 2 months ago
• chung-lab / SCAFE
  Single Cell Analysis of Five'Ends
  ☆50Updated last year
• jdekanter / CHETAH
  scRNA-seq cell type identification
  ☆43Updated 6 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆81Updated 3 years ago