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97 search results found

Nextflow ⭐ 2,055

A DSL for data-driven computational pipelines

Bioconda Recipes ⭐ 1,488

Conda recipes for the bioconda channel.

Official code repository for GATK versions 4 and up

Scispacy ⭐ 1,391

A full spaCy pipeline and models for scientific/biomedical documents.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Hicexplorer ⭐ 149

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

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

Quantum Mechanical Bespoke Force Field Derivation Toolkit

Plant Seg ⭐ 74

A tool for cell instance aware segmentation in densely packed 3D volumetric images

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.

Cell_blast ⭐ 67

A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.

A package for designing compact and comprehensive capture probe sets.

Mulled - Automatized Containerized Software Repository

Long-read splice alignment with high accuracy

Grabseqs ⭐ 44

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

A package to annotate protein sequences

2020plus ⭐ 39

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

Integron_finder ⭐ 37

Bioinformatics tool to find integrons in bacterial genomes

An opinionated Cromwell orchestration manager.

dcHiC: Differential compartment analysis for Hi-C datasets

Population-wide Deletion Calling

Bioconda.github.io ⭐ 31

Bioconda is a distribution of bioinformatics software realized as a channel for the versatile package manager Conda.

Wochenende ⭐ 30

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

Conda Env Builder ⭐ 30

Build and maintain multiple custom conda environments all in one place.

Computational Analysis of Novel Drug Opportunities

Fast and flexible semi-supervised learning for peptide detection in Python

Phyloprofile ⭐ 27

A phylogenetic profile analysis tool

Contact_map ⭐ 27

Contact map analysis for biomolecules; based on MDTraj

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Discover ⭐ 23

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

A lightweight library for working with PAF (Pairwise mApping Format) files

Paccmann_datasets ⭐ 20

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

Echolocator ⭐ 20

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

Panoptes ⭐ 19

Monitor computational workflows in real time

Mapping-Assisted Targeted-Assembly for Metagenomics

Bactpipe ⭐ 17

BACTpipe: An assembly and annotation pipeline for bacterial genomics

A package for designing activity-informed nucleic acid diagnostics for viruses.

API for HOMER in R for Genomic Analysis using Tidy Conventions

Saffrontree ⭐ 14

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Cataloguer ⭐ 12

Easy-to-use R wrappers for the eQTL Catalogue's API (both with tabix and the REST API).

Srijan Gsoc 2020 ⭐ 12

Healthcare-Researcher-Connector Package: Federated Learning tool for bridging the gap between Healthcare providers and researchers

Reproducible_bioinformatics ⭐ 10

Workshop material for BioC Asia 2019

Containers Rules Manuscript ⭐ 10

Recommendations to contenarized your bioinformatics software

CBMPy is a Python based platform for constraint based modelling and analysis.

Hla Polysolver ⭐ 9

Fork of the Polysolver project

Derives consensus sequences from a set of long noisy reads by clustering and error correction.

Riboraptor ⭐ 9

Tool for ribo-seq analysis

Kgwasflow ⭐ 8

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

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)

Schicexplorer ⭐ 8

Single-cell Hi-C data analysis toolbox

Documentation on St. Jude Cloud.

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Albatradis ⭐ 7

Comparative TraDIS analysis

Epigraphdb ⭐ 6

Examples on using EpiGraphDB

Uorf Tools ⭐ 6

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

Biojava Notebooks ⭐ 6

BioJava examples in Jupyter Notebooks

Streaming de Bruijn and Compact de Bruijn Graph Algorithms

Reproducible Research Guidelines ⭐ 6

Guidelines for accountable and reproducible computational research

Assemblycomparator2 ⭐ 6

🦠📇 Compare microbial assemblies

FOCUS: An Agile Profiler for Metagenomic Data

Dambi Hpc Guide ⭐ 5

Basic and Advanced usage of High-Performance Computing in Bioinformatics

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.

build and run deployable Jupyter notebooks

Bioflows is an easy to use package for running bioinformatics workflows.

Imgqfinder ⭐ 4

The official python version of ImGQfinder: http://imgqfinder.niifhm.ru/ A tool that finds gquadruplexes and imotifs.

Diag_pipelines ⭐ 4

Pipelines dealing with high throughput sequencing data for microbiology diagnostic procedures. Documentation available at http://metagenlabdiag-pipelines.readthedocs.io/en/ and Docker images at https://hub.docker.com/r/metagenlab/diag_pipelines

Insert genes into genomes to aid synthetic test data generation

Ribose Map ⭐ 4

Enanofastq ⭐ 3

A FASTQ lossless compression algorithm especially designed for nanopore sequencing FASTQ files.

Multisample DNAseq variant calling pipeline for use in diagnostics

singularity environment manager (application to NGS and bioinformatics)

Cubi_demux ⭐ 3

Demultiplexing utility, companion to flowcelltool.

Bifrost Archive ⭐ 3

Bacterial Surveillance platform, focused on QC in Denmark

Software for finding transcription factor binding motifs using knockout controls, in CUT&RUN data.

Interactive results viewer for maltExtract

Bioinformatics_pipeline_with_snakemake_2019 06 27 ⭐ 2

Intro to snakemake for bioinformatics - WestGrid Research Computing Summer School 2019 - University of British Columbia

Ypkpathway ⭐ 2

Automatic pathway assembly with the YeastPathwayKit

Damage parameter estimation for ancient DNA

PISPINO (PIpits SPIN-Off tools): Bioinformatics toolkits for processing NGS data

Bioinfo Notebook ⭐ 2

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

Organdiet ⭐ 2

Metagenomics pipeline for human diet analysis using organelles genomes

Docker image for latest BioBuilds release

Milestone ⭐ 1

bacterial strain identification

Rna Count Kallisto ⭐ 1

Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto

a bioinformatics fungal pipeline

Snakemakereproducibility ⭐ 1

Bioinformatics Pipeline Building meeting - Demo 2018-12-13 on reproducibility using Snakemake and Conda

Lncrnadiscovery ⭐ 1

Snakemake pipeline for lncRNA discovery and quantification

Conda Chem Bioinfo Pkgs ⭐ 1

Conda recipes for chem/bioinformatics packages

Snp_crispr ⭐ 1

SNP-targeted CRISPR sgRNA design pipeline

Rapid, accurate annotations of Plasmids from Illumina NGS reads

Tools For Cancer Genome Analysis ⭐ 1

Installation and usage for various tools for cancer genomics

Condathis ⭐ 1

Condathis: run any CLI tool on a Conda Environment

Gtexsnake ⭐ 1

A fully concurrent pipeline for querying transcript-level GTEx data in specific tissues

Azolla_genus_metagenome ⭐ 1

This project aims do describe and explore the metagenomes of fern species of the genus Azolla.

Single_snake_sequencing ⭐ 1

A Snakemake workflow for standardised sc/snRNAseq analysis

Pipeliner ⭐ 1

RNA-seq pipeline implemented using nextflow

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