maxplanck-ie / snakepipesLinks
Customizable workflows based on snakemake and python for the analysis of NGS data
☆397Updated last week
Alternatives and similar repositories for snakepipes
Users that are interested in snakepipes are comparing it to the libraries listed below
Sorting:
- RNA-seq workflow using STAR and DESeq2☆346Updated 2 months ago
- Package for fetching metadata and downloading data from SRA/ENA/GEO☆345Updated this week
- parallel fastq-dump wrapper☆299Updated 2 years ago
- Application for making ENCODE Blacklists☆327Updated 4 years ago
- GTEx & TOPMed data production and analysis pipelines☆386Updated 2 months ago
- A collection of scripts and notes related to genomics and bioinformatics☆217Updated last week
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆426Updated last year
- ChIP-seq peak-calling, QC and differential analysis pipeline.☆226Updated 3 weeks ago
- ENCODE ChIP-seq pipeline☆275Updated last year
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆434Updated 3 months ago
- zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs☆286Updated last year
- ATAC-seq peak-calling and QC analysis pipeline☆213Updated this week
- Intro to ChIPseq using HPC☆316Updated 2 years ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆443Updated 10 months ago
- Fast and accurate gene fusion detection from RNA-Seq data☆251Updated last month
- A tool to find sequencing data and metadata from public databases.☆592Updated last year
- SUPPA: Fast quantification of splicing and differential splicing☆284Updated last week
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆455Updated last year
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆274Updated 2 years ago
- Tools for handling Unique Molecular Identifiers in NGS data sets☆528Updated 4 months ago
- ☆279Updated 3 weeks ago
- Performant Pythonic GenomicRanges☆489Updated 2 weeks ago
- This Snakemake pipeline implements the GATK best-practices workflow☆260Updated 2 years ago
- 10x Genomics Single Cell Analysis☆437Updated 9 months ago
- Download FASTQ files from SRA or ENA repositories.☆350Updated 4 months ago
- Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.☆393Updated last week
- genes and genomes at your fingertips☆402Updated last month
- Quick mining and visualization of NGS data by integrating genomic databases☆268Updated 2 years ago
- This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster☆172Updated 4 years ago
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel☆180Updated last week