Topic: bioinformatics-pipeline Goto Github

👇 Here are 621 public repositories matching this topic...

algbio / ggcat
bioinformatics-pipeline,Compacted and colored de Bruijn graph construction and querying
Organization: algbio
bioinformatics bioinformatics-pipeline sequencing de-novo-assembly debruijn-graph genome-assembly rust

aureme / metage2metabo
bioinformatics-pipeline,From annotated genomes to metabolic screening in large scale microbiotas
Organization: aureme
Home Page: https://metage2metabo.readthedocs.io
bioinformatics bioinformatics-pipeline metabolic-models

bacalhau-project / bacalhau
bioinformatics-pipeline,Compute over Data framework for public, transparent, and optionally verifiable computation
Organization: bacalhau-project
Home Page: https://docs.bacalhau.org
p2p distributed iot bioinformatics-pipeline data-analysis data-engineering data-science decentralized video-processing batch-processing

biowdl / tasks
bioinformatics-pipeline,A collection of reusable WDL tasks. Category:Other
Organization: biowdl
Home Page: https://biowdl.github.io/tasks/
tasks wdl bioinformatics bioinformatics-pipeline workflow wdl-tasks

bobeobibo / phigaro
bioinformatics-pipeline,Phigaro is a scalable command-line tool for predicting phages and prophages
User: bobeobibo
bioinformatics bioinformatics-tool bioinformatics-pipeline bioinformatics-analysis biological-data-analysis phage phages prophage genomics genomic-data-analysis

bystrogenomics / bystro
bioinformatics-pipeline,Bystro genetic analysis (annotation, filtering, statistics)
Organization: bystrogenomics
bioinformatics bioinformatics-algorithms bioinformatics-analysis bioinformatics-databases bioinformatics-pipeline bioinformatics-scripts genomics genomics-search

cansysbio / consensustme
bioinformatics-pipeline,ConsensusTME Gene Sets and R Script
Organization: cansysbio
cancer-genomics bioinformatics-pipeline deconvolution immune tumour-microenvironment consensus-algorithm

cbg-ethz / v-pipe
bioinformatics-pipeline,V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Organization: cbg-ethz
Home Page: https://cbg-ethz.github.io/V-pipe/
ngs snakemake conda biohackeu20 virus sequencing bioinformatics bioinformatics-pipeline biohackcovid20 sars-cov-2

chanzuckerberg / czid-web
bioinformatics-pipeline,Infectious Disease Sequencing Platform
Organization: chanzuckerberg
Home Page: https://czid.org/
infectious-diseases genomics sequencing metagenomic science next-generation-sequencing research biology virology bioinformatics

cihga39871 / pipelines.jl
bioinformatics-pipeline,A lightweight and powerful Julia package for computational pipelines and workflows.
User: cihga39871
computational-pipelines pipelines julia workflow bioinformatics bioinformatics-pipeline workflows ruffus pipeline snakemake

databio / pypiper
bioinformatics-pipeline,Python toolkit for building restartable pipelines
Organization: databio
Home Page: http://pypiper.databio.org
pipeline python-toolkit python bioinformatics bioinformatics-pipeline

flowhub-team / wholegenomesequencing-wgs
bioinformatics-pipeline,Whole Genome Sequencing analysis, WGS analysis
User: flowhub-team
bioinfomatics bioinformatics-pipeline genome wes wgs whole-genome-sequencing

gencorefacility / variant-calling-pipeline-gatk4
bioinformatics-pipeline,Variant Calling Pipeline Using GATK4 and Nextflow
Organization: gencorefacility
bioinformatics bioinformatics-pipeline nextflow variant-calling gatk4 genomics

genomiqueens / eoulsan
bioinformatics-pipeline,A pipeline and a framework for NGS analysis (RNA-seq and scRNA-seq)
Organization: genomiqueens
Home Page: http://www.outils.genomique.biologie.ens.fr/eoulsan2
rna-seq java cloud-computing-clusters analysis workflow-engine bioinformatics-pipeline

grailbio / reflow
bioinformatics-pipeline,A language and runtime for distributed, incremental data processing in the cloud
Organization: grailbio
bioinformatics-pipeline scientific-computing language runtime data-science cloud-computing aws analysis-pipeline golang

gregoryschwartz / too-many-cells
bioinformatics-pipeline,Cluster single cells and analyze cell clade relationships with colorful visualizations.
User: gregoryschwartz
Home Page: https://gregoryschwartz.github.io/too-many-cells/
single-cell visualization single-cell-analysis single-cell-rna-seq bioinformatics-pipeline bioinformatics-algorithms

guyteichman / rnalysis
bioinformatics-pipeline,Analyze your RNA sequencing data without writing a single line of code
User: guyteichman
Home Page: https://guyteichman.github.io/RNAlysis/
rna-seq rna-seq-analysis rna-seq-pipeline rnaseq bioinformatics bioinformatics-pipeline bioinformatics-tool bioinformatics-analysis transcriptomics smallrna

hillerlab / make_lastz_chains
bioinformatics-pipeline,Portable solution to generate genome alignment chains using lastz
Organization: hillerlab
bioinformatics bioinformatics-pipeline genomics

hillerlab / toga
bioinformatics-pipeline,TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
Organization: hillerlab
bioinformatics genomics bioinformatics-pipeline genome-annotation

jetbrains-research / snakecharm
bioinformatics-pipeline,Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
Organization: jetbrains-research
snakemake pycharm intellij-plugins python intellij bioinformatics-pipeline bioinformatics-tool

karchinlab / open-cravat
bioinformatics-pipeline,A modular annotation tool for genomic variants
Organization: karchinlab
variant-annotations variant-annotation variant-analysis genomics genomic-data-analysis bioinformatics bioinformatics-pipeline bioinformatics-tool annotation-tool python

kundajelab / atac_dnase_pipelines
bioinformatics-pipeline,ATAC-seq and DNase-seq processing pipeline
Organization: kundajelab
atac-seq dnase-seq bioinformatics-pipeline

lynnlangit / gcp-for-bioinformatics
bioinformatics-pipeline,GCP for Bioinformatics Researchers
User: lynnlangit
Home Page: https://www.youtube.com/playlist?list=PL4Q4HssKcxYvcixWS08UFaYIH7y4IAV0z
gcp bioinformatics bioinformatics-pipeline bioinformatics-analysis genomics bioinformatics-researchers google nextflow google-batch

maayanlab / zika-rnaseq-pipeline
bioinformatics-pipeline,An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
Organization: maayanlab
Home Page: http://bit.ly/2g4hCe7
rna-seq rna-seq-analysis pipeline notebook jupyter-notebook bioinformatics-pipeline

mitongs / mtoolbox
bioinformatics-pipeline,A bioinformatics pipeline to analyze mtDNA from NGS data
Organization: mitongs
Home Page: http://sourceforge.net/projects/mtoolbox/?source=navbar
bioinformatics-pipeline mtdna mt-variant mitochondrial-variants mtoolbox

ngless-toolkit / ngless
bioinformatics-pipeline,NGLess: NGS with less work
Organization: ngless-toolkit
Home Page: https://ngless.embl.de
haskell bioinformatics bioinformatics-pipeline samtools bwa next-generation-sequencing fastq-format fastq science ngs

nickjcroucher / gubbins
bioinformatics-pipeline,Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
User: nickjcroucher
Home Page: http://nickjcroucher.github.io/gubbins/
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

nsalomonis / altanalyze
bioinformatics-pipeline,AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
User: nsalomonis
Home Page: http://www.altanalyze.org
rna-seq-data alternative-splicing scrna-seq-data bioinformatics-pipeline clustering pathway-analysis network-analysis splicing-quantification splicing-visualization python

omaroakheart / nphase
bioinformatics-pipeline,Ploidy agnostic phasing pipeline and algorithm
User: omaroakheart
polyploid phasing bioinformatics bioinformatics-pipeline

pyladies-brazil / grupo-estudo-bioinformatica
bioinformatics-pipeline,Repositório do grupo de estudo de Bioinformática da rede de comunidades das PyLadies Brasil.
Organization: pyladies-brazil
bioinformatics bioinformatics-pipeline bioinformatics-analysis biopython rosalind estudo

r3fang / snapatac
bioinformatics-pipeline,Analysis Pipeline for Single Cell ATAC-seq
User: r3fang
single-cell-atac-seq single-cell-analysis bioinformatics-pipeline epigenetics machine-learning-algorithms sequencing

sagnikbanerjee15 / finder
bioinformatics-pipeline,A fully automated gene annotator from RNA-Seq expression data
User: sagnikbanerjee15
gene-annotations rna-seq gtf finder protein-sequences changepoint-detection gene-models transcripts predict-genes bioinformatics

saketkc / pysradb
bioinformatics-pipeline,Package for fetching metadata and downloading data from SRA/ENA/GEO
User: saketkc
Home Page: https://saketkc.github.io/pysradb
bioinformatics ncbi-sra ncbi-sra-archive sratoolkit bioinformatics-pipeline sra ena

sanger-pathogens / ariba
bioinformatics-pipeline,Antimicrobial Resistance Identification By Assembly
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/ariba/
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / artemis
bioinformatics-pipeline,Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/Artemis
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / assembly_improvement
bioinformatics-pipeline,Improve the quality of a denovo assembly by scaffolding and gap filling
Organization: sanger-pathogens
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / circlator
bioinformatics-pipeline,A tool to circularize genome assemblies
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/circlator/
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / iva
bioinformatics-pipeline,de novo virus assembler of Illumina paired reads
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/iva/
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / roary
bioinformatics-pipeline,Rapid large-scale prokaryote pan genome analysis
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/Roary
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

sanger-pathogens / snp-sites
bioinformatics-pipeline,Finds SNP sites from a multi-FASTA alignment file
Organization: sanger-pathogens
Home Page: http://sanger-pathogens.github.io/snp-sites/
genomics sequencing next-generation-sequencing research bioinformatics bioinformatics-pipeline global-health infectious-diseases pathogen

scipipe / scipipe
bioinformatics-pipeline,Robust, flexible and resource-efficient pipelines using Go and the commandline
Organization: scipipe
Home Page: https://scipipe.org
scientific-workflows bioinformatics-pipeline workflow go dataflow pipeline cheminformatics bioinformatics fbp scipipe

shujiahuang / ilus
bioinformatics-pipeline,A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
User: shujiahuang
whole-genome-sequencing variant-calling bioinformatics bioinformatics-pipeline pipeline

stjudecloud / oliver
bioinformatics-pipeline,An opinionated Cromwell orchestration manager.
Organization: stjudecloud
Home Page: https://stjudecloud.github.io/oliver
genomics cromwell workflow oliver wdl workflow-execution hpc next-generation-sequencing bioinformatics bioinformatics-pipeline

twoxes / awesome-structural-bioinformatics
bioinformatics-pipeline,Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
User: twoxes
molecular-informatics chemistry machine-learning deep-learning cheminformatics biology quantum-chemistry docking protein alphafold

uc-bd2k / grein
bioinformatics-pipeline,GREIN : GEO RNA-seq Experiments Interactive Navigator
Organization: uc-bd2k
Home Page: https://shiny.ilincs.org/grein
rna-seq geo bioinformatics-pipeline bioinformatics-analysis rna-seq-pipeline rna-seq-data rna-seq-analysis graphical-interface r shiny-apps

urmi-21 / pyrpipe
bioinformatics-pipeline,Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
User: urmi-21
rna-seq rna-seq-pipeline ncbi-sra bioinformatics bioinformatics-pipeline bioinformatics-analysis python rna-seq-workflows conda bioconda

vanheeringen-lab / seq2science
bioinformatics-pipeline,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.
Organization: vanheeringen-lab
Home Page: https://vanheeringen-lab.github.io/seq2science
snakemake bioinformatics bioinformatics-pipeline atac-seq rna-seq chip-seq reproducible-research ngs pipeline sra workflows fastq

yangwu91 / r2g
bioinformatics-pipeline,A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
User: yangwu91
bioinformatics ncbi-sra homology orthology bioinformatics-pipeline phylogenetics gene-sequence-retrieval

yichaoou / hemtools
bioinformatics-pipeline,HemTools: a collection of NGS pipelines and bioinformatic analyses
User: yichaoou
Home Page: https://hemtools.readthedocs.io
ngs ngs-analysis python r hpc-applications bioinformatics-pipeline bash data-visualization

yupenghe / methylpy
bioinformatics-pipeline,WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
User: yupenghe
bioinformatics-pipeline epigenetics dna-methylation nome-seq functional-genomics differential-methylation nome-seq-data calling-dmrs