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https://github.com/gibsramen/qadabra

Snakemake workflow for comparison of differential abundance ranks
bioinformatics differential-abundance machine-learning metagenomics microbiome pipeline snakemake workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: May 04, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 60
  • Committers: 3
  • Issues: 16
  • Pull Requests: 23
  • Owner: biocore
  • Stars: 13
  • Forks: 4
  • Packages: 1
  • Downloads: 8
https://github.com/cihga39871/pipelines.jl

A lightweight and powerful Julia package for computational pipelines and workflows.
bioinformatics bioinformatics-pipeline computational-pipelines julia pipeline pipelines ruffus snakemake workflow workflows
Added: over 1 year ago - Last Synced: about 1 year ago - Created: March 23, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Julia
  • Commits: 155
  • Committers: 2
  • Issues: 13
  • Pull Requests: 1
  • Owner: cihga39871
  • Stars: 45
  • Forks: 2
  • Packages: 1
https://github.com/snakemake/snakefmt

The uncompromising Snakemake code formatter
bioinformatics black code codeformatter fmt formatter python snakemake
Added: over 1 year ago - Last Synced: about 1 year ago - Created: February 28, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 400
  • Committers: 18
  • Issues: 72
  • Pull Requests: 72
  • Owner: snakemake
  • Stars: 139
  • Forks: 24
  • Packages: 2
  • Downloads: 9,127
https://github.com/rickgelhausen/hribo

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 characterization.
bioinformatics prokaryotes ribosome-profiling snakemake
Added: over 1 year ago - Last Synced: about 1 year ago - Created: August 30, 2018

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 752
  • Committers: 6
  • Issues: 29
  • Pull Requests: 26
  • Owner: RickGelhausen
  • Stars: 8
  • Forks: 3
  • Packages: 1
  • Downloads: 9
https://github.com/epigen/mr.pareto

MR. PARETO - Modules & Recipes for Pragmatic Augmentation of Research Efficiency Towards Optimum
automation bioinformatics biomedical data-science framework snakemake workflows
Added: over 1 year ago - Last Synced: about 1 year ago - Created: March 28, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: /projects/review
  • Commits: 37
  • Committers: 2
  • Issues: 2
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 3
  • Forks: 0
  • Packages: 0
https://github.com/epigen/mixscape_seurat

A Snakemake workflow for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.
bioinformatics biomedical-data-science perturbation-analysis sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: April 14, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 20
  • Committers: 2
  • Issues: 4
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 2
  • Forks: 0
  • Packages: 0
https://github.com/epigen/dea_seurat

A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
bioinformatics biomedical-data-science differential-expression-analysis scrna-seq single-cell snakemake snrna-seq visualization volcano-plot workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: April 20, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 19
  • Committers: 2
  • Issues: 10
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 10
  • Forks: 10
  • Packages: 0
https://github.com/biocore/qadabra

Snakemake workflow for comparison of differential abundance ranks
bioinformatics differential-abundance machine-learning metagenomics microbiome pipeline snakemake workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: May 04, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 96
  • Committers: 4
  • Issues: 41
  • Pull Requests: 51
  • Owner: biocore
  • Stars: 13
  • Forks: 4
  • Packages: 0
https://github.com/epigen/dea_limma

A Snakemake workflow for performing and visualizing differential expression analyses (DEA) on NGS data powered by the R package limma.
atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom r rna-seq scrna-seq snakemake statistics visualization volcano-plot workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: August 12, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 47
  • Committers: 3
  • Issues: 9
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 14
  • Forks: 0
  • Packages: 0
https://github.com/joybio/multiprime

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))
bioinformatics multiplexpcr panel pcr python snakemake tngs viterbi
Added: over 1 year ago - Last Synced: about 1 year ago - Created: September 05, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 326
  • Committers: 2
  • Issues: 17
  • Pull Requests: 0
  • Owner: joybio
  • Stars: 226
  • Forks: 16
  • Packages: 1
  • Downloads: 81
https://github.com/remi-gau/bidsgnostic

BIDS app to view a dataset content and the events file content
bids bids-apps eeg fnirs ieeg meg mri pet quality-control snakebids snakemake visualization
Added: over 1 year ago - Last Synced: about 1 year ago - Created: December 31, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 159
  • Committers: 2
  • Issues: 10
  • Pull Requests: 32
  • Owner: Remi-Gau
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/zavolanlab/mirflowz

Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
bioinformatics isomirs mirna snakemake workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: March 06, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 141
  • Committers: 8
  • Issues: 62
  • Pull Requests: 47
https://github.com/openomics/ervx

Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with bulk RNA
endogenous-retrovirus-expression herv human mouse pipeline quality-control singularity snakemake workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: March 07, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 47
  • Committers: 2
  • Issues: 1
  • Pull Requests: 0
  • Owner: OpenOmics
  • Stars: 1
  • Forks: 1
  • Packages: 0
https://github.com/daylily-informatics/daylily

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.
aws bioinformatics bioinformatics-pipeline budgeting ec2 ephemeral genomic-data-analysis giab human-genome informatics ngs parallel-cluster scalable scaling slurm snakemake snv-call wgs
Added: over 1 year ago - Last Synced: about 1 year ago - Created: April 29, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 313
  • Committers: 12
  • Issues: 0
  • Pull Requests: 17
https://github.com/epigen/spilterlize_integrate

A Snakemake workflow to split, filter, normalize, integrate and select highly variable features of count matrices resulting from experiments with sequencing readout (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including diagnostic visualizations.
atac-seq batch-effect bioinformatics biomedical-data-science chip-seq count-matrix dimensionality-reduction integration ngs normalization pipeline rna-seq snakemake visualization workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: June 28, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 22
  • Committers: 2
  • Issues: 7
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 8
  • Forks: 0
  • Packages: 0
https://github.com/gibsramen/xebec

Snakemake pipeline for microbiome diversity effect size benchmarking
bioinformatics microbiome pipeline snakemake
Added: over 1 year ago - Last Synced: about 1 year ago - Created: March 22, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 119
  • Committers: 2
  • Issues: 0
  • Pull Requests: 14
  • Owner: gibsramen
  • Stars: 5
  • Forks: 2
  • Packages: 1
  • Downloads: 51
https://github.com/bishop-laboratory/rlpipes

RLPipes: A standardized R-loop-mapping pipeline.
bioinformatics ngs pipeline r-loop snakemake
Added: over 1 year ago - Last Synced: about 1 year ago - Created: June 03, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 246
  • Committers: 4
  • Issues: 70
  • Pull Requests: 21