GitHub topics: bioinformatics-pipeline

Repositories

hms-immunology/RNA_QC_APP

RNA-seq Quality Control and Preprocessing Tool - Interactive Shiny application for comprehensive RNA sequencing data validation, quality assessment, filtering, and normalization. Developed at Harvard Medical School Department of Immunology for global research use. Topics

Language: R - Size: 11 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0

replikation/MPOA

Mask Pathogens for Outbreak Analysis

Language: Nextflow - Size: 1.31 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 2 - Forks: 0

ImagoXV/NanoASV

NanoASV official repo

Language: Shell - Size: 86.4 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 9 - Forks: 3

weygoldt/wavetracker Fork of tillraab/wavetracker

Track fundamental frequencies of multiple wave-type electric fish on electrode grid recordings

Language: Python - Size: 1.13 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 2

gabrielvpina/viralquest

A user-friendly pipeline for viral diversity analysis and characterization.

Language: Python - Size: 44 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

chanzuckerberg/czid-web

Infectious Disease Sequencing Platform

Language: TypeScript - Size: 466 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 85 - Forks: 25

medvir/VirMet

Set of tools for viral metagenomics.

Language: Python - Size: 1.19 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 14 - Forks: 5

GuyTeichman/RNAlysis

Analyze your RNA sequencing data without writing a single line of code

Language: Python - Size: 797 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 135 - Forks: 13

milaboratory/platforma

Platforma SDK

Language: TypeScript - Size: 22.6 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 17 - Forks: 2

niekwit/damid-seq

DamMapper: Snakemake workflow for DamID-Seq analysis

Language: Python - Size: 83.2 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 4 - Forks: 0

bacalhau-project/bacalhau

Community-driven, simple, yet powerful framework for fast, cost-effective distributed Compute over Data.

Language: Go - Size: 191 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 808 - Forks: 97

V-Z/hybseq-scripts

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

Language: Shell - Size: 2.35 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 4 - Forks: 2

mansikath/Variant-calling

Repository for variant calling utilizing bioinformatics tools and databases

Size: 10.7 KB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

RoySoumik23/AutoMutSig_Pipeline

The automation pipeline processes mutation and clinical data, aligning and cleaning the inputs before performing a detailed analysis. It enables visualization and interpretation of mutation signatures with a focus on specific genes and cancer subtypes.

Language: R - Size: 106 KB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 1

JoshuaIszatt/phunky

Nanopore long read assembly data pipeline for phage genomes

Language: Python - Size: 151 KB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

Mansur090909/Drug_Potency_PredictionML

Allows users to investigate a target protein / disease, and generate a machine learning model to predict potency in any compound (in SMILES format) against that target as represented by the pIC50 metric.

Language: Python - Size: 226 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

tjpel/ProteomicsAnalysisPipeline

A highly customizable proteomics analysis pipeline for TMT and Olink data.

Language: Python - Size: 69.1 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 3 - Forks: 0

incsteps/nf-cachebrowser

A Nextflow plugin that provides a web-based interface for visualizing and exploring Nextflow pipeline executions directly in your browser.

Language: Groovy - Size: 337 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 2

biowdl/tasks

A collection of reusable WDL tasks. Category:Other

Language: WDL - Size: 1.77 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 87 - Forks: 30

rpratam/amr

This repository will help you to perform bioinformatics analysis on sequencing data from different sequencing platform (ONT, Illumination)

Size: 526 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

zjnolen/PopGLen

Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.

Language: Python - Size: 18.6 MB - Last synced at: 4 days ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 1

Snakemake-Profiles/lsf

Snakemake profile for running jobs on an LSF cluster

Language: Python - Size: 166 KB - Last synced at: 5 days ago - Pushed at: 10 months ago - Stars: 37 - Forks: 22

CHETHAN562/reflow

A simple CLI deployment manager for Next.js apps using Docker (Nginx, Blue-Green) on Linux VPS.

Language: Go - Size: 101 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

KarchinLab/open-cravat

A modular annotation tool for genomic variants

Language: JavaScript - Size: 9.25 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 121 - Forks: 33

Yuxuanliu-HZAU/HybSuite

An integrated pipeline for hybrid capture phylogenomics from reads to trees

Language: Shell - Size: 15.8 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 3 - Forks: 0

DelusionalSimon/Barrel-aged_GNN

Reproducible glycoinformatics pipeline for automated machine learning experiments

Language: Jupyter Notebook - Size: 13.8 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

yodeng/runjob

runjob is a program for managing a group of related jobs running on a compute cluster

Language: Python - Size: 1.19 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 10 - Forks: 4

gbif/hp-asean

Biodiversity Informatics and Geospatial Analysis, ASEAN Centre for Biodiversity

Language: SCSS - Size: 37.1 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 1

lynnlangit/gcp-for-bioinformatics

GCP for Bioinformatics Researchers

Language: Jupyter Notebook - Size: 89.9 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 263 - Forks: 70

ilmn-mouse-cecal/ribozap

Tool for creating additional probes

Language: Python - Size: 110 KB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 0

Marcos-Fernando/AnnoTEP

AnnoTEP - a platform for the annotation of transposable elements in plants

Language: Perl - Size: 205 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 3 - Forks: 0

stjude-rust-labs/sprocket

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Language: Rust - Size: 1020 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 72 - Forks: 12

SPerekrestova/pill_checker

Provides a powerful medicine pack analysis using ML and NLP to achieve accurate recognition of active ingredients

Language: Python - Size: 1.15 MB - Last synced at: 6 days ago - Pushed at: 9 days ago - Stars: 3 - Forks: 1

andrewgull/MGERT

Mobile Genetic Elements Retrieving Tool

Language: Python - Size: 1.99 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 15 - Forks: 5

Preetam2303/tcga-biomarker-pipeline

R pipeline for TCGA transcriptomics biomarker discovery with ML & SHAP

Language: R - Size: 41 KB - Last synced at: 1 day ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

ronaldsoft/MARIA

A novel ultrafast and multithreaded bioinformatics toolkit built in Golang for cleaning raw sequencing data from Illumina, Oxford Nanopore, PacBio, and Ion Torrent platforms.

Language: Go - Size: 2.42 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 0

IdoBar/HPC_SNP_calling_documentation

SNP calling pipeline for clonal Ascochyta rabiei

Language: HTML - Size: 7.06 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

barricklab/seabreeze Fork of ira-zibbu/seabreeze-ltee-analysis

seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies

Language: Python - Size: 20 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 1

BCCDC-PHL/plasmid-screen

Screen plasmids for carbapenemase resistance genes, and classify using MOB Suite

Language: Python - Size: 93.8 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 1 - Forks: 0

TurakhiaLab/ROADIES

Tool for fully-automated inference of species trees from raw genome assemblies

Language: Python - Size: 279 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 33 - Forks: 3

gloknar/scRNA-Seq_Protocol_Updated_Xiao_et_al

Optimization of Xiao et al.'s protocol for scRNA-seq analysis in R 4.X

Language: HTML - Size: 682 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

nodrogluap/tamor

Illumina Dragen cancer genome and transcriptome analysis automation using Snakemake

Language: Python - Size: 381 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 7 - Forks: 1

mobidic/MobiDL

MobidicWDL workflows

Language: WDL - Size: 559 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 5 - Forks: 5

sanger-pathogens/snp-sites

Finds SNP sites from a multi-FASTA alignment file

Language: C - Size: 14.7 MB - Last synced at: 15 days ago - Pushed at: over 4 years ago - Stars: 259 - Forks: 49

datirium/workflows

CWL based Bioinformatics Workflows

Language: Common Workflow Language - Size: 3.4 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 16 - Forks: 16

DeplanckeLab/ASAP

ASAP : Automated Single-cell Analysis Pipeline

Size: 170 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 26 - Forks: 10

ShujiaHuang/ilus

A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.

Language: Python - Size: 855 KB - Last synced at: 14 days ago - Pushed at: 18 days ago - Stars: 133 - Forks: 34

Yasas1994/vcat

A tool for adding taxonomic annotations to virus contigs, mapping reads to virus genomes and much more.

Language: Python - Size: 2.26 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 4 - Forks: 0

saketkc/pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

Language: Python - Size: 7.09 MB - Last synced at: 16 days ago - Pushed at: 4 months ago - Stars: 328 - Forks: 65

scipipe/scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

Language: Go - Size: 1.06 MB - Last synced at: 15 days ago - Pushed at: 10 months ago - Stars: 1,096 - Forks: 72

sabifo4/fasta-phylip-partitions

Convert from fasta to phylip format and generate partitioned data if needed

Language: Perl - Size: 48.8 KB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 3 - Forks: 0

SWAROOP006/NGS-Variant-Calling

This project focuses on identifying somatic variants in whole-genome sequencing (WGS) data from tongue cancer samples and cell lines. The workflow leverages industry-standard tools for alignment, quality control, and variant calling, specifically targeting chromosomes 6 and 7 of the human genome.

Language: HTML - Size: 1.94 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 0 - Forks: 0

SWAROOP006/Machine-Learning-in-Bioinformatics-using-WEKA

Used WEKA machine learning tool to analyze the Breast cancer data and also study Protein characteristics using SMO, naïve byes and IBk models also, data bias was removed using bagging and stacking. R program was used to extract the character-specific protein sequences using the R package PROTr and peptide.

Language: R - Size: 129 KB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 1 - Forks: 0

hammerlab/biokepi

Bioinformatics Ketrew Pipelines

Language: OCaml - Size: 1.87 MB - Last synced at: 2 days ago - Pushed at: over 3 years ago - Stars: 28 - Forks: 4

oicr-gsi/shesmu

Decision-driven action launching system

Language: Java - Size: 38.2 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 8 - Forks: 4

sirine-b/VariantAInalyser

VariantAInalyser is a comprehensive platform that combines traditional bioinformatics with generative AI to streamline genomic variant analysis from VCF files. It eliminates the need to juggle multiple specialised tools by providing an all-in-one solution for variant analysis, interpretation, and reporting.

Language: Jupyter Notebook - Size: 7.43 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 0 - Forks: 0

GregorySchwartz/too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.

Language: Haskell - Size: 22.3 MB - Last synced at: 11 days ago - Pushed at: 7 months ago - Stars: 111 - Forks: 18

iPsychonaut/EGAP

Entheome Genome Assembly Pipeline (EGAP)

Language: Python - Size: 22.8 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 1 - Forks: 0

jeszyman/cfdna-cna

Language: R - Size: 273 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 0 - Forks: 0

bioinfonupeb/transcriptomic_analysis_lep

Transcriptomic analysis.

Size: 2.93 KB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 0 - Forks: 0

sanger-pathogens/ariba

Antimicrobial Resistance Identification By Assembly

Language: Python - Size: 12 MB - Last synced at: 22 days ago - Pushed at: over 1 year ago - Stars: 175 - Forks: 55

CompOmics/meta-proteome-analyzer

MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.

Language: TSQL - Size: 607 MB - Last synced at: 10 days ago - Pushed at: almost 5 years ago - Stars: 30 - Forks: 10

whl-usc/rna2d3d

Scripts and reference files relevant to the computational analysis of data generated by crosslink-ligation based experiments.

Language: Python - Size: 52 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 1 - Forks: 0

databio/pypiper

Python toolkit for building restartable pipelines

Language: Python - Size: 1.63 MB - Last synced at: 13 days ago - Pushed at: 3 months ago - Stars: 45 - Forks: 9

grailbio/reflow

A language and runtime for distributed, incremental data processing in the cloud

Language: Go - Size: 6.96 MB - Last synced at: 5 days ago - Pushed at: over 1 year ago - Stars: 967 - Forks: 52

marco315176/Analisis-de-Genomas-Virales

Análisis de genomas virales obtenidos por secuenciación de genoma completo con illumina

Language: Shell - Size: 85.9 KB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 0 - Forks: 0

montilab/nf-gwas-pipeline

A Nextflow Genome-Wide Association Study (GWAS) Pipeline

Language: R - Size: 5.25 MB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 35 - Forks: 20

m-jahn/TnSeq-pipe

TnSeq data processing workflow

Language: Perl - Size: 265 MB - Last synced at: 18 days ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 2

biopatternsg/biopatternsg

biopatternsg is a system that builds gene regulatory networks from a basic collection of biological objects, gathering and processing PubMed abstracts, using Internet available informational resources like Mesh, GeneOntology, UniProt, PDB and others, and that uses java and logical engines like prolog to integrate and analyse them.

Size: 230 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 0 - Forks: 1

vanheeringen-lab/seq2science

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.

Language: Python - Size: 1.39 GB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 156 - Forks: 28

cbg-ethz/V-pipe

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

Language: Jupyter Notebook - Size: 17.4 MB - Last synced at: 14 days ago - Pushed at: 30 days ago - Stars: 136 - Forks: 46

Elliot-Chan-120/NOCTURNAL-v2.1.0

NOCTURNAL: Exploring the dark chemical space. A ChEMBL navigation-aided interface aiming to accelerate early drug discovery by scouting biological targets, building ML models on potency vs. molecular fingerprints, predicting compound potency, and generating optimized drug analogs using MutaGen, an original stochastic-heuristic algorithm system.

Language: Python - Size: 5.65 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 0

renatosantos98/ont-benchmark

Supporting data for the publication "Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing"

Language: Jupyter Notebook - Size: 199 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 1

stjude-rust-labs/sprocket-action

Run Sprocket WDL document validation as part of a CI/CD pipeline with GitHub Actions.

Language: Shell - Size: 387 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 1

miano-fc/MaxQuant-Tools

Tools for preprocessing and normalizing results of MaxQuant experiments and their respective controls from a run by normalizing data from the output peptides.txt file.

Language: Python - Size: 51.8 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

sanger-pathogens/circlator

A tool to circularize genome assemblies

Language: Python - Size: 25.7 MB - Last synced at: 14 days ago - Pushed at: about 1 year ago - Stars: 242 - Forks: 57

AuReMe/metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

Language: Jupyter Notebook - Size: 36.3 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 57 - Forks: 7

ricardo-romero-ochoa/kinasepred

Kinase Inhibitor Bioactivity & Toxicity Prediction Platform

Language: Python - Size: 18.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

twoXes/awesome-structural-bioinformatics

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.

Language: Python - Size: 31.1 MB - Last synced at: 24 days ago - Pushed at: about 2 years ago - Stars: 71 - Forks: 10

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.

Language: Python - Size: 340 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 23 - Forks: 2

niekwit/crispr-screens

Snakemake workflow for CRISPR-Cas9 screen analysis

Language: Python - Size: 35.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 1

open2c/distiller-sm

a Snakemake version of distiller - the Open2C Hi-C mapping workflow

Language: Python - Size: 131 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 3

MDU-PHL/bohra

A pipeline for bioinformatics analysis of bacterial genomes

Language: Nextflow - Size: 356 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 28 - Forks: 4

CogDisResLab/drugfindR

Repository holding the code for the drugfindR R package

Language: R - Size: 7.13 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 3

Umeshkumarku1/Zoonoticus

Zoonoticus is a comprehensive tool for predicting zoonotic potential, antimicrobial resistance risk, and virulence profiles of bacterial genomes. Powered by Zento, it helps researchers rapidly identify bacteria capable of crossing species barriers and posing public health threats.

Language: Python - Size: 2.68 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0