Alternatives and similar repositories for scrnaseq

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

• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆216Updated last week
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆226Updated last week
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆327Updated 4 years ago
• Xinglab / rmats-turbo
  ☆281Updated last month
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆286Updated last year
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆316Updated 2 years ago
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆275Updated last year
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆331Updated 2 weeks ago
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆233Updated 2 months ago
• CebolaLab / RNA-seq
  Step-by-step analysis pipeline for RNA-seq data
  ☆156Updated 2 years ago
• hbctraining / Intro-to-DGE
  ☆210Updated 3 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆348Updated this week
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆300Updated 2 years ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆486Updated 6 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆285Updated 3 weeks ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆302Updated last month
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆253Updated 2 months ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆437Updated 9 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆244Updated last week
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆270Updated 3 weeks ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆332Updated this week
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆388Updated 2 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated last week
• hbctraining / Intro-to-bulk-RNAseq
  Introduction to bulk RNA-seq
  ☆126Updated 6 months ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆435Updated last year
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆268Updated 11 months ago
• hbctraining / Investigating-chromatin-biology-ChIPseq
  ☆99Updated 2 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆426Updated last year
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆530Updated 4 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆268Updated 2 years ago