dropSeqPipe
RNASeq pipeline
A pre-processing workflow for SingleCell RNASeq data from raw sequencing data to final count matrix with QC plots.
A SingleCell RNASeq pre-processing snakemake workflow
147 stars
9 watching
47 forks
Language: Python
last commit: about 2 years ago
Linked from 1 awesome list
condadrop-seqdropseqdropseqtoolsmultiqcpicardpipelineplotreference-genomescrb-seqscrbseqsnakemakestarumiyaml
seandavi/awesome-single-cellRelated projects:
| Repository | Description | Stars |
|---|---|---|
 kharchenkolab/dropest | A software pipeline for analyzing single-cell RNA-seq data from droplet-based experiments | 88 |
 griffithlab/rnaseq_tutorial | An educational tutorial and working demonstration pipeline for RNA-seq analysis on the cloud | 1,345 |
 dowell-lab/rnaseq-flow | A Nextflow pipeline for processing RNA-seq data | 8 |
 crazyhottommy/rna-seq-analysis | A collection of resources and tools for analyzing RNA sequencing data using Python and Snakemake workflows | 951 |
 elementolab/sctcrseq | An open-source Python pipeline for processing single-cell RNA sequencing data to recover T cell receptor sequences. | 26 |
 pachterlab/kallistobustools | A workflow for pre-processing single-cell RNA-seq data using Kallisto and Bustools. | 115 |
 snakemake-workflows/single-cell-rna-seq | A workflow generator for single-cell RNA-seq data analysis | 100 |
 nextflow-io/rnaseq-nf | A pipeline for quantifying genomic features from short read data using Nextflow and various software components. | 74 |
 yeolab/outrigger | Automates detection and quantification of alternative splicing events from RNA seq data using graph databases. | 65 |
 bcbio/bcbio-nextgen | A high-level configuration file drives parallel variant calling and analysis on sequencing data. | 995 |
 sdparekh/zumis | A fast and flexible pipeline for processing RNA-seq data with UMIs | 275 |
 cbcrg/kallisto-nf | A tool suite implementing Kallisto and Sleuth RNA-seq analysis pipelines in Nextflow | 22 |
 guigolab/grape-nf | Automated RNA-seq analysis pipeline using Nextflow and Docker/Singularity containers | 37 |
 marchinilab/dropsim | A tool for simulating single-cell RNA sequencing data for research purposes. | 5 |
 nf-core/rnaseq | An RNA sequencing analysis pipeline that performs quality control, trimming, alignment, and quantification of gene expression from raw sequencing data. | 941 |