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137 search results found

Bioconda Recipes ⭐ 1,488

Conda recipes for the bioconda channel.

Getting Started With Genomics Tools And Resources ⭐ 872

Unix, R and python tools for genomics and data science

A cross-platform command-line tool for executing jobs in parallel

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Bpipe - a tool for running and managing bioinformatics pipelines

Biosyntax ⭐ 184

Syntax highlighting for computational biology

Edamontology ⭐ 108

EDAM is an ontology of bioscientific data analysis and data management. EDAM concentrates on topics, operations, types of data, and data formats related to analysis, modelling, optimisation, and data life-cycle in biosciences, and in other research and science-based applications.

Genome_updater ⭐ 99

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Bionitio ⭐ 92

Demonstrating best practices for bioinformatics command line tools

Smk Simple Slurm ⭐ 80

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

Cut Runtools 2.0 ⭐ 62

CUT&RUN and CUT&Tag data processing and analysis

Packages ⭐ 56

Aim to be the bioinformatics repository with more and newer packages

Teamteri ⭐ 48

Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure

Microbiomebestpracticereview ⭐ 45

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Cytomine Bootstrap ⭐ 35

Cytomine Community Edition Legacy

Picardmetrics ⭐ 34

🚦 Run Picard on BAM files and collate 90 metrics into one file.

The specification of the MMTF format for biological structures

Bioinftraining ⭐ 29

Repository for bioinformatics training at the Norwegian Veterinary Institute

genEra is an easy-to-use, low-dependency command-line tool that estimates the age of the last common ancestor of protein-coding gene families.

Orthoevolution ⭐ 28

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

Bio.brew ⭐ 27

A tiny package manager for crucial unix and bioinformatics tools

VAPiD: Viral Annotation and Identification Pipeline

Ctdna Pipeline ⭐ 24

A simplified pipeline for ctDNA sequencing data analysis

Common_analyses ⭐ 20

Repository of common bioinformatics scripts

the z in bioinformatics

Jaxbd2k Shortcourse ⭐ 19

This repository contains course materials from JAX-BD2K workshop.

Peptide Prediction List ⭐ 18

Collects software dedicated to predicting specific properties of peptides

Team Rosalind Project ⭐ 18

This is the main repository for the HackBio'2020 Virtual Internship Experience ❤️

Bioinformaticsmaterials ⭐ 18

Syllabus and materials for bioinformatics lecture + lab

Bioinformatics Tools ⭐ 14

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS

Prophage_tracer ⭐ 13

Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment

Bio Workshop 18 ⭐ 13

Pawsey workshop: containers for bioinformatics

Compbio Gists ⭐ 12

Computational Biology & Bioinformatics Resources

Pipernaseq ⭐ 12

A comprehensive pipeline for RNAseq data analysis

Epigenomicstutorial Ismb2017 ⭐ 11

Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague

Motifscan ⭐ 11

A motif discovery tool to detect the occurrences of known motifs

Graphical GUI for Docker (Bioconductor, R, Cytoscape, NetworkBMA)

Deepvariant On Spark ⭐ 11

DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.

A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)

🔲⚛️ A collection of molecular modelling tools for UCSF Chimera

Genomics_adventure ⭐ 10

Workshop on Genomics - Genomics Adventure

Containers Rules Manuscript ⭐ 10

Recommendations to contenarized your bioinformatics software

Ng Meta Profiler ⭐ 10

Profiler for metagenomics based on NGLess

H2o Curated Data ⭐ 9

Semi-hand curated command-line option data for many CLI programs, geared toward bioinformatics tools. Shell completion scripts are also available.

A fast, easy way to present complex bioinformatics pipelines to biologists

RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (preliminary version at https://arxiv.org/abs/2301.09200)

BEAR: viral diagnostic analysis pipeline for SARS-CoV-2

Documentation on St. Jude Cloud.

P2rank Framework ⭐ 6

The central entry point to the P2Rank project with links to the individual projects, including references to documentation, datasets, etc.

Workflows ⭐ 6

Snakemake workflows for best practice genomic analysis

A short course on Bioinformatics for Evolutionary Biology

Shell_intro_for_bioinformatics_stg ⭐ 6

Intro to Shell for Bioinformatics - with STG examples

Donut: automated Circos visualization of multiple fasta files within a docker image

Automated RNA-seq pipeline for lncRNA indentification

Easy_circos ⭐ 5

easy_circos is a simple conda package that aims on rapidly and easily creating minimal circos configurations templates based on input data.

Fastq To Bam ⭐ 5

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

BTW – Bioinformatics Through Windows: an easy-to-install package to analyze 16S rRNA data

uorf4u is a bioinformatics tool for conserved upstream ORF annotation.

Akutils_ubuntu_installer ⭐ 5

Bioinformatics packages I like and use. All installed by one convenient script.

Efficient Variant Analysis

Bioinfougrp ⭐ 4

OIST Bioinfo user group

Piperiboseq ⭐ 4

A comprehensive pipeline for Ribo-seq data analysis

Ribose Map ⭐ 4

Coronavirus Genomics Datasette ⭐ 4

Recode_rnaseq_pipeline ⭐ 4

A parallelised pipeline for the analysis of RNA sequencing data. This repository is part of Imperial College London's ReCoDE project, which aims to support teaching and learning in research computing and data science.

Bioinformatics ⭐ 4

Bioinformatics N' Stuff

Structurepipelines ⭐ 4

Pipelines to run STRUCTURE using multiple front-ends (CLUMPAK+StrAuto, Structure_threader)

This is the official site for JASPER (Jellyfish based Assembly Sequence Polisher for Error Reduction)

Beacon (灯塔) of liulab

Commoncompute ⭐ 3

Common compute resources for Sage data scientists

Multiomicanalysis ⭐ 3

Genome-centric Multi-omic Analysis Workflow for the Marinimicrobia paper

Bioinformatics Profile ⭐ 3

Tooling for profiling bioinformatics pipelines

Interproscan Docker ⭐ 3

A Dockerfile and associated tools for deploying containerized InterProScan5.

Bioscript ⭐ 3

Some shell, perl, python script for my own bioinformatics tasks.

Hybseq Scripts ⭐ 3

Set of scripts to process HybSeq target enrichment HTS data (on computing grids).

Unix_tips_etc ⭐ 3

A collection of scripts/commands for working in UNIX environments

Nessie.jl ⭐ 3

Nonlocal Electrostatics in Structured Solvents

Seminar Bioinformatics Rna Seq ⭐ 3

Applied Bioinformatics on the Example of Gene Expression Analysis using Unix and freely available Open Source Tools

Blacklister ⭐ 3

Improve your metagenomic reference sequence: Simple adapter and contamination FASTA masking using bowtie2 and bedtools

Gh Actions Lint ⭐ 3

GitHub Action to run nf-core code linting on a Nextflow pipeline

Sequence Stats ⭐ 3

Generate statistics from FASTQ and FASTA files. Also manipulate sequences such as renaming contigs and converting FASTQ to FASTA. Written in Bash. All in one place.

Gito: A Docker image based on research software good practices for building containers of bioinformatics software

Ng2018_bioinformatics ⭐ 3

Bioinformatics_scripts ⭐ 3

A collection of scripts commonly used while running bioinformatics analyses on the Tulane University Cypress HPC

Cubi_demux ⭐ 3

Demultiplexing utility, companion to flowcelltool.

Au Bootcamp Git Intro ⭐ 3

Git introduction for Auburn University Bioinformatics Bootcamp

Repet Slurm ⭐ 3

SLURM-ready bash scripts to run the complete REPET pipeline

Single Cell Allele-Specific Analysis - Containerized tool for genotyping, phasing, mapping bias correction, and generation of single cell allele-specific counts

Docker Stacks ⭐ 3

Stacks is a software pipeline for building loci from short-read sequences - Now in a Docker

RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

Introme prioritises coding and noncoding splice-altering variants for clinical variant interpretation

Refactoring_bioinformatics_pipelines ⭐ 3

Refactoring implementations of common bioinformatics pipelines for scalability, using Docker, MagicBLAST and gRPC

Bioinfo Notebook ⭐ 2

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

Shellflow ⭐ 2

Shell script like workflow managmenet software

Bcc2020cle ⭐ 2

Command Line Essentials for Bioinformaticians - Training material for BCC2020

Repository for the Data Hub project

Wgs_pipeline ⭐ 2

Bacterial whole genome sequencing (WGS) analysis

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