Alternatives and similar repositories for toolkit

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

• cbg-ethz / SCICoNE
  Single-cell copy number calling and event history reconstruction.
  ☆27Updated 7 months ago
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆110Updated 8 months ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆58Updated 2 months ago
• natsuhiko / rasqual
  Robust Allele Specific Quantification and quality controL
  ☆40Updated 3 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆55Updated 4 years ago
• mcvickerlab / varCA
  Use an ensemble of variant callers to call variants from ATAC-seq data
  ☆23Updated 2 months ago
• lcmmichielsen / scHPL
  ☆35Updated 5 months ago
• BuysDB / SingleCellMultiOmics
  Tools which deal with multiple single cell measurements
  ☆24Updated last month
• atarashansky / self-assembling-manifold
  The Self-Assembling-Manifold (SAM) algorithm.
  ☆44Updated last year
• 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
• nskvir / RepEnrich
  RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆27Updated 3 years ago
• HorvathLab / NGS
  Next-Gen Sequencing tools from the Horvath Lab
  ☆44Updated 2 weeks ago
• dphansti / mango
  chia pet analysis software
  ☆25Updated 6 years ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• nf-core / spatialvi
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…
  ☆66Updated last month
• dpeerlab / Harmony
  Harmony framework for connecting scRNA-seq data from discrete time points
  ☆50Updated last year
• yjzhang / split-seq-pipeline
  ☆22Updated 5 years ago
• cole-trapnell-lab / cicero-release
  ☆59Updated 11 months ago
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• christacaggiano / celfie
  cfDNA cell type of origin estimation
  ☆31Updated last year
• ebi-gene-expression-group / scanpy-scripts
  Scripts for using scanpy
  ☆37Updated 4 months ago
• kundajelab / ataqc
  ☆17Updated 6 years ago
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆70Updated 8 months ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆74Updated 2 years ago
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆32Updated 2 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 years ago
• Xinglab / CLAM
  CLIP-seq Analysis of Multi-mapped reads
  ☆31Updated 4 years ago
• KCCG / rageseq
  RAGE-seq scripts
  ☆18Updated 3 years ago
• ernstlab / full_stack_ChromHMM_annotations
  Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes
  ☆37Updated last year