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Search results for python snakemake

91 search results found

Rna Seq Analysis ⭐ 614

RNAseq analysis notes from Ming Tang

Snakepipes ⭐ 359

Customizable workflows based on snakemake and python for the analysis of NGS data

ATLAS - Three commands to start analyzing your metagenome data

Rna Seq Star Deseq2 ⭐ 282

RNA-seq workflow using STAR and DESeq2

Metagem ⭐ 155

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Dna Seq Gatk Variant Calling ⭐ 138

This Snakemake pipeline implements the GATK best-practices workflow

Dropseqpipe ⭐ 134

A SingleCell RNASeq pre-processing snakemake workflow

Seq2science ⭐ 132

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Snakefmt ⭐ 131

The uncompromising Snakemake code formatter

Multiprime ⭐ 123

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))

Dna Seq Varlociraptor ⭐ 76

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.

Grenepipe ⭐ 75

A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Rna Seq Kallisto Sleuth ⭐ 63

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Snakefiles ⭐ 58

🐍 Snakefiles for common RNA-seq data analysis workflows.

Snakecharm ⭐ 58

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

Pyflow Chipseq ⭐ 55

a snakemake pipeline to process ChIP-seq files from GEO or in-house

Pytest Workflow ⭐ 52

Configure workflow/pipeline tests using yaml files.

Sv Callers ⭐ 52

Snakemake-based workflow for detecting structural variants in genomic data

Pyflow Atacseq ⭐ 37

ATAC-seq snakemake pipeline

Hecatomb ⭐ 36

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

Tourmaline ⭐ 32

Amplicon sequence processing workflow using QIIME 2 and Snakemake

Ngs_pipeline ⭐ 31

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Snakemake profile for running jobs on an LSF cluster

Pubrunner ⭐ 29

A framework for keeping biomedical text mining result up-to-date

Zavolan-Lab Automated RNA-Seq Pipeline

Atacseq_pipeline ⭐ 25

Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.

Technology-invariant pipeline for spatial-omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

Phylociraptor ⭐ 23

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

mapping pipeline for ancient DNA

Explore the impacts of 24/7 Carbon-Free Energy PPAs

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

Use an ensemble of variant callers to call variants from ATAC-seq data

Snek5000 ⭐ 20

🐍 Python framework for Nek5000 🚀

snakemake pipeline for Hi-C post-processing

Pigx_rnaseq ⭐ 19

Pipeline for RNAseq

Kgwasflow ⭐ 19

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Metameta ⭐ 18

Vesselexpress ⭐ 17

🔬🖥 Automated Blood Vasculature Analysis of 3D Light-Sheet Image Volumes

Cookiecutter Reproducible Research ⭐ 16

A cookiecutter template for reproducible research projects using Python, Snakemake, and Pandoc.

Snakemake skeleton - Build workflows with Snakemake

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

Pyflow Rnaseq ⭐ 15

RNAseq pipeline based on snakemake

Nbpipeline ⭐ 14

Snakemake-like pipeline manager for reproducible Jupyter Notebooks

Snakemake Novice Bioinformatics ⭐ 14

Introduction to Snakemake for Bioinformatics

Snakebids ⭐ 14

Snakemake + BIDS

Ngs Test Data ⭐ 14

A workflow for creating small NGS test data sets, useful for continuous integration.

Snakemake Wrappers ⭐ 14

🐍 Snakemake wrappers for bioinformatics.

Snakemake workflow for comparison of differential abundance ranks

Flexible omics pipeline

Ngs Pipeline ⭐ 12

Pipeline for Somatic Variant Calling with WES and WGS data

Mikropml Snakemake Workflow ⭐ 12

Snakemake template for building reusable and scalable machine learning pipelines with mikropml

Genome Seek ⭐ 12

Clinical Whole Genome Sequencing Pipeline

Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!

Preprocessing pipeline for (sc)ATAC data

Pigx_bsseq ⭐ 10

bisulfite sequencing pipeline from fastq to methylation reports

Snakemake based framework for NGS data analysis and management

Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees

MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis

Cascabel ⭐ 10

Automated pipeline for amplicon sequence analysis

Enrichment_analysis ⭐ 10

A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.

Solar And Wind Potentials ⭐ 10

Estimation of solar and wind power generation potentials in Europe.

A Sphinx extension for Snakemake workflows

Unsupervised_analysis ⭐ 9

A general purpose Snakemake workflow to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.

Riboraptor ⭐ 9

Tool for ribo-seq analysis

Triti Map ⭐ 9

A Snakemake-based pipeline for gene mapping in Triticeae.

💻💻💻 A commandline tool for analysis of big biological data sets for distributed HPC clusters.

Multiple_sclerosis_proj ⭐ 8

Data analysis platform/structure, machine learning/AI project for multiple sclerosis

We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional charact

Snakemake_rnaseq ⭐ 8

A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)

Snakemake Workflow Fermi Lat ⭐ 7

A Snakemake workflow for Fermi-LAT data reduction

Lescroart2023 ⭐ 7

Archived code for analyses in "Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus" (Lescroart et al. 2023, MBE)

JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes

🗺️ MAPP is a computational method which enables identification of binding motifs for RNA-binding proteins that shape pre-mRNA processing under specific conditions.

Rnaseq_workflow ⭐ 6

snakemake workflow for bulk RNA-seq workflow using STAR-edgeR

Uorf Tools ⭐ 6

uORF-Tools are a workflow and a collection of tools for the analysis of 'Upstream Open Reading Frames' (short uORFs)

Salmonscholar ⭐ 6

Don't get drowned in the flood of scientific publications. As a salmon, climb up to the stream.

Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)

Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)

SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

Snakemake pipeline for microbiome diversity effect size benchmarking

Updated version of PAQR, which was previously available in the PAQR_KAPAC joint repository.

Nbis Meta ⭐ 5

A snakemake workflow for metagenomic projects

Generate the UMI count matrix from CEL-Seq2 sequencing data

Snakemake Slurm Tutorial ⭐ 5

Working example of snakemake tutorial using UAB Cheaha computing cluster via SLURM scheduler

AllMine, a flexible pipeline for Allele Mining. Develloped at INRA's GAFL unit :

Metagenomics ⭐ 5

Snakemake workflow for functional analysis of metagenomic WGS read data.

A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.

Germline_variant_snakemake ⭐ 5

Snakemake workflow to call germline variant

Genome_tracks ⭐ 5

A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.

Serpent Methylation Pipeline ⭐ 5

An efficient, documented, reproducible Snakemake methylation analysis pipeline for BS-seq and EM-seq samples, including cfDNA.

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