Search Results - RepositoryStats

snakemake snakemake

588

2.4k

mit

18

This is the development home of the workflow management system Snakemake. For general information, see

snakemake reproducibility workflow-management

Created 2019-10-04

5,520 commits to main branch, last one 11 hours ago

RNA-seq-analysis crazyhottommy

309

992

mit

78

RNAseq analysis notes from Ming Tang

rna-seq snakemake

Created 2015-08-26

322 commits to master branch, last one 3 years ago

multiPrime joybio

38

447

mit

27

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)

pcr tngs panel python viterbi snakemake multiplexpcr bioinformatics

Created 2022-09-05

336 commits to main branch, last one about a month ago

pypsa-eur PyPSA

276

410

unknown

18

PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

pypsa energy snakemake energy-model energy-system power-systems energy-systems energy-system-model

Created 2017-10-11

5,498 commits to master branch, last one 7 hours ago

snakepipes maxplanck-ie

87

395

unknown

20

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

ngs hi-c rna-seq atac-seq chip-seq workflow snakemake bisulfite-sequencing

Created 2016-03-23

4,059 commits to master branch, last one 5 months ago

atlas metagenome-atlas

100

383

bsd-3-clause

14

ATLAS - Three commands to start analyzing your metagenome data

assembly snakemake annotation metagenomics genomic-binning functional-annotation taxonomic-classifications

Created 2016-11-30

2,824 commits to main branch, last one 14 days ago

rna-seq-star-deseq2 snakemake-workflows

210

338

mit

12

RNA-seq workflow using STAR and DESeq2

deseq2 snakemake sciworkflows reproducibility gene-expression-analysis

Created 2017-10-06

148 commits to master branch, last one 10 months ago

dna-seq-gatk-variant-calling snakemake-workflows

145

250

mit

9

This Snakemake pipeline implements the GATK best-practices workflow

gatk snakemake sciworkflows reproducibility genomic-variant-calling

Created 2018-06-28

125 commits to main branch, last one 3 years ago

metaGEM franciscozorrilla

47

228

mit

5

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

mags snakemake metabolism microbiome metagenomics bioinformatics gut-microbiome systems-biology metabolic-models microbial-ecology metabolic-modeling computational-biology flux-balance-analysis genome-scale-metabolic-model metagenome-assembled-genomes

Created 2018-06-14

669 commits to master branch, last one 8 months ago

sunbeam sunbeam-labs

42

169

unknown

7

A robust, extensible metagenomics pipeline

snakemake metagenomics reproducible-research

Created 2016-04-28

1,759 commits to main branch, last one 7 months ago

snakefmt snakemake

30

162

mit

5

The uncompromising Snakemake code formatter

fmt code black python formatter snakemake codeformatter bioinformatics

Created 2020-02-28

442 commits to master branch, last one 13 days ago

seq2science vanheeringen-lab

28

156

mit

4

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.

ngs sra fastq rna-seq atac-seq chip-seq pipeline snakemake workflows bioinformatics reproducible-research bioinformatics-pipeline

Created 2019-07-11

1,483 commits to master branch, last one about a year ago

docs snakemake-workflows

25

153

mit

13

Documentation of the Snakemake-Workflows project

snakemake snakemake-workflows

Created 2017-05-22

24 commits to master branch, last one 3 years ago

smk-simple-slurm jdblischak

19

153

cc0-1.0

6

A simple Snakemake profile for Slurm without --cluster-config

slurm snakemake bioinformatics snakemake-profile

Created 2021-05-01

59 commits to main branch, last one 9 months ago

dropSeqPipe Hoohm

47

147

cc-by-sa-4.0

8

A SingleCell RNASeq pre-processing snakemake workflow

umi plot star yaml conda picard dropseq multiqc scrbseq drop-seq pipeline scrb-seq snakemake dropseqtools reference-genome

Created 2016-08-02

333 commits to master branch, last one 2 years ago

sequana sequana

27

146

bsd-3-clause

6

Sequana: a set of Snakemake NGS pipelines

ngs pacbio de-novo rna-seq coverage sequanix taxonomy snakemake variant-calling

Created 2016-03-07

6,421 commits to main branch, last one about a month ago

V-pipe cbg-ethz

47

135

apache-2.0

9

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

hiv ngs conda virus genomics sarscov2 snakemake sars-cov-2 sequencing biohackeu20 biohackeu21 biohackeu22 biohackcovid20 bioinformatics bioinformatics-pipeline

Created 2017-04-10

1,200 commits to master branch, last one 22 days ago

grenepipe moiexpositoalonsolab

22

96

gpl-3.0

3

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.

snakemake ancient-dna variant-calls pool-sequencing variant-calling snakemake-workflow population-genetics evolve-and-resequence genomic-variant-calling

Created 2020-05-06

621 commits to master branch, last one 7 days ago

dna-seq-varlociraptor snakemake-workflows

41

85

mit

7

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 Var...

snakemake sciworkflows varlociraptor reproducibility genomic-variant-calling

Created 2020-01-17

457 commits to master branch, last one 8 days ago

sv-callers GooglingTheCancerGenome

35

80

apache-2.0

3

Snakemake-based workflow for detecting structural variants in genomic data

wgs workflow snakemake sv-calling bioinformatics cancer-genomics hpc-applications somatic-variants germline-variants structural-variants

Created 2017-04-10

475 commits to master branch, last one about a month ago

panoptes panoptes-organization

19

72

mit

5

Monitor computational workflows in real time

snakemake workflows bioinformatics reproducible-research

Created 2019-11-11

85 commits to master branch, last one 10 months ago

tibanna 4dn-dcic

27

69

mit

13

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/ doc...

aws cwl wdl conda docker pipelines snakemake aws-lambda cwl-workflow wdl-workflow bioinformatics aws-step-function snakemake-workflow

Created 2016-07-14

4,023 commits to master branch, last one 4 months ago

rna-seq-kallisto-sleuth snakemake-workflows

45

68

mit

4

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

sleuth rna-seq kallisto snakemake sciworkflows reproducibility differential-expression

Created 2018-12-12

181 commits to main branch, last one 15 days ago

pytest-workflow LUMC

10

67

agpl-3.0

6

Configure workflow/pipeline tests using yaml files.

wdl test yaml pytest miniwdl testing cromwell nextflow pipeline workflow snakemake wdl-devtools pytest-plugin workflow-testing

Created 2018-12-05

1,234 commits to develop branch, last one 10 months ago

snakemake-econ-r lachlandeer

13

63

mit

2

reproducible research project template for R using Renv and snakemake with an econ application

renv workflow economics snakemake reproducibility snakemake-workflow reproducible-research

Created 2018-03-20

326 commits to master branch, last one 2 years ago

snakecharm JetBrains-Research

7

61

mit

5

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

python pycharm intellij snakemake intellij-plugins bioinformatics-tool bioinformatics-pipeline

Created 2019-01-11

1,109 commits to master branch, last one 4 months ago

cookiecutter-snakemake-workflow snakemake-workflows

37

58

mit

3

A cookiecutter template for Snakemake workflows

snakemake snakemake-workflows cookiecutter-template

Created 2017-05-22

24 commits to master branch, last one 3 years ago

hecatomb shandley

12

57

mit

5

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

virome snakemake viral-metagenomes

Created 2019-10-14

907 commits to main branch, last one 2 months ago

CompareM2 cmkobel

3

56

gpl-3.0

2

🦠📇 Microbial genomes-to-report pipeline

hpc pbs conda slurm archaea bacteria bioconda apptainer snakemake prokaryotes metagenomics bioinformatics clinical-research genomes-to-report microbial-genomics

Created 2019-12-10

1,967 commits to master branch, last one 29 days ago

atacseq_pipeline epigen

2

51

mit

3

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

ngs bash python atac-seq pipeline workflow snakemake bioinformatics biomedical-data-science

Created 2021-03-22

173 commits to main branch, last one 24 days ago