GitHub topics: snakemake-pipeline

Repositories

XuegongLab/neoguider

NeoGuider, neoepitope detection using advanced feature engineering

Language: Python - Size: 12.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 3 - Forks: 1

AndreaMariani-AM/ChIPseq_snakemake

ChIPseq pipeline for Pasini's lab written in snakemake

Language: Python - Size: 117 KB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

ht-diva/pqtl_pipeline_finemap

Fine mapping analysis within the pQTL pipeline project

Language: R - Size: 27.4 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

open2c/distiller-sm

a Snakemake version of distiller - the Open2C Hi-C mapping workflow

Language: Python - Size: 113 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 4 - Forks: 3

ctubbs750/cbs-db3-annotate

Component in the cbs-db multi-repo designed to produce all CTCF Binding Site annotations included in the database.

Language: Jupyter Notebook - Size: 298 KB - Last synced at: 12 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

OpenOmics/modr

An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

Language: Python - Size: 689 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 1

skchronicles/RNA-seek

A comprehensive quality-control and quantification RNA-seq pipeline

Language: Python - Size: 10.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 13

Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

Language: Python - Size: 5.73 MB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 0

ht-diva/MR_instruments_selection

Language: R - Size: 681 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

ruppinlab/tcga-wgs-kraken-microbial-quant

Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data

Language: Python - Size: 21.7 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1

ht-diva/pqtl_pipeline

Language: Python - Size: 277 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

petebachant/snakemake-tutorial

Running the Snakemake tutorial with Calkit.

Language: Python - Size: 33.2 KB - Last synced at: about 20 hours ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

fritzbayer/snakemake-with-R

Simple template for running snakemake with R

Language: R - Size: 35.2 KB - Last synced at: 13 days ago - Pushed at: about 2 years ago - Stars: 11 - Forks: 1

J22160/DualRNASeq_Pipeline

The DualRNASeq Pipeline is a comprehensive, automated workflow designed to analyze host-pathogen dualRNA-Seq data, offering insights into gene expression dynamics during infection. Its modular Snakemake framework ensures reproducibility, scalability, and seamless execution on local machines, HPC clusters, or cloud platforms.

Language: Python - Size: 39.1 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Moha-cm/AutoRNASeq

Simplified RNA-Seq Insights with automation

Language: HTML - Size: 4.61 MB - Last synced at: 23 days ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

Programa-de-neoplasias-linfoides/rnaseq_virginia

RNASeq Pipeline for Virginia Amador group

Language: Python - Size: 81.1 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

ac1513/MAGqual

MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards

Language: Python - Size: 116 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 4 - Forks: 0

ht-diva/meta_pipeline

Language: Python - Size: 66.4 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

smith-chem-wisc/Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data

Language: C# - Size: 34.8 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 7 - Forks: 11

InstitutoTodosPelaSaude/respat_snakemake

Pipeline for analyses of multiple pathogens, like SARS-CoV-2 with positivity rate analyses

Language: Python - Size: 36.7 MB - Last synced at: 11 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

cmkobel/mspipeline1

🪆🦖 A snakemake wrapper around Nesvilab's FragPipe-CLI. In a perfect world, this pipeline was based on Sage.

Language: Python - Size: 1.78 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

pmenzel/ont-assembly-snake

Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools

Language: Python - Size: 99.6 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 17 - Forks: 2

Reynaaaaaaaaaaa/Python_dataprocessing_pipeline

Python & R multi-language data analysis pipeline

Language: R - Size: 458 KB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

CarolinaPB/population-structural-var-calling-smoove

population structural variant calling with smoove

Language: Python - Size: 1.84 MB - Last synced at: 8 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 3

Rendrick27/AlignEvaluator

Language: Python - Size: 23.6 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

pmenzel/score-assemblies

Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)

Language: Python - Size: 1.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 22 - Forks: 1

raveancic/scRNAaltas_TNBC_mm

Language: Python - Size: 22.5 KB - Last synced at: 4 months ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 2

brimittleman/apaQTL

Project for apaQTL MS. The workflowr project apaQTL by brimittleman

Language: Shell - Size: 74.8 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 2

ESR-NZ/human_genomics_pipeline

A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

Language: Python - Size: 13.2 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 23 - Forks: 19

AngryMaciek/snakemake_fastqc 📦

A small snakemake pipeline to perform quality analysis of RNA-Seq data with FastQC.

Language: Python - Size: 42 KB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

fatmakahveci/milestone

bacterial strain identification

Language: Python - Size: 8.78 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Dfupa/meTAline

Taxonomic assignation pipeline implementation in Snakemake for shotgun genome sequencing

Language: Python - Size: 134 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

AngryMaciek/snakemake_vast_tools 📦

My personal snakemake pipeline for VAST-TOOLS execution

Language: Python - Size: 61.5 KB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

AngryMaciek/snakemake_deeptools 📦

Small snakemake pipeline to explore RNA-Seq data with deepTools.

Language: Python - Size: 31.3 KB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

AngryMaciek/snakemake_suppa2 📦

A snakemake workflow to perform Alternative Splicing analysis from RNA-Seq with SUPPA2.

Language: Python - Size: 2.89 MB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 1

AngryMaciek/snakemake_qdgedtu 📦

RNA-Seq data analysis: Quantification, Differential Gene Expression, Differential Transcripts Usage

Language: R - Size: 83 KB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

svpipaliya/bulk-rnaseq

This repo contains scripts and workflows for performing bulk transcriptomics analyses

Language: R - Size: 184 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

SammedMandape/NIST

Work at NIST: snakemake workflow to get short tandem repeats from WGS GIAB samples. R script for downstream processing and concordance

Language: R - Size: 72.3 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

michalbukowski/rnaseq-pipeline-1

Simple Snakemake RNA-Seq pipeline

Language: Python - Size: 942 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

CCBR/RNA-seek Fork of skchronicles/RNA-seek

A comprehensive quality-control and quantification RNA-seq pipeline

Language: Python - Size: 10.4 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

Related Keywords

snakemake-pipeline 53 snakemake 22 bioinformatics 16 bioinformatics-pipeline 12 rna-seq 12 python 8 snakemake-workflow 7 pipeline 7 singularity 4 quality-control 4 r 4 conda 4 hi-c 3 interval 3 genomics 3 computational-biology 3 metagenomics 3 proteomics 2 gene-fusions 2 gene-expression 2 annotation-tool 2 snakemake-rna-seq 2 mamba 2 transcriptomics 2 metagenomic-pipeline 2 alternative-splicing 2 genome-assembly 2 nanopore-sequencing 2 nanopore-assembly 2 bacterial-genome-analysis 2 mapping 2 gwas-summary-statistics 2 qtl 2 hic 2 graph 1 strain 1 bacterial-strain 1 bioconda 1 conda-environment 1 bioinformatics-analysis 1 bioinformatics-scripts 1 shotgun-sequencing 1 bioinformatics-tool 1 differential-gene-expression 1 shell-scripting 1 survivor 1 vep 1 genome-analysis 1 cellranger 1 pbs 1 scrna 1 scrna-seq-analysis 1 cohort-analysis 1 exome-pipeline 1 gatk-bestpractices 1 gatk4 1 illumina 1 nvidia-clara-parabricks 1 nvidia-gpu 1 bacteria 1 bacterial-genomes 1 scrna-seq 1 fpkm 1 gene 1 rna-seq-analysis 1 rna-seq-data 1 rna-seq-pipeline 1 cutntag 1 epigenetics 1 pipelines 1 freebayes 1 short-reads 1 variant-calling 1 gbs 1 genotyping-by-sequencing 1 scaffolding 1 annotation 1 snakemake-pipelines 1 snakemake-workflows 1 differential-transcripts 1 bioconductor 1 dge 1 dge-analysis 1 miniconda 1 miniconda3 1 pandas 1 python3 1 rnaseq-analysis 1 rnaseq-pipeline 1 salmon 1 salmon-deseq2 1 reproducible-research 1 workflow 1 snakemake-tutorials 1 vcf 1 alternative-polyadenylation 1 cleavage-sites 1 alternative-splicing-analysis 1 differential-expression-analysis 1 direct-rna-sequencing 1