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504 search results found

10x Genomics Reads Simulator

Rustybam ⭐ 38

bioinformatics toolkit in rust

Chm Eval ⭐ 37

de novo virus assembler of Illumina paired reads

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

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.

An opinionated Cromwell orchestration manager.

Hicpeaks ⭐ 36

A Python implementation for BH-FDR and HiCCUPS

Genome Annotation Pipeline ⭐ 36

Genome annotation pipeline

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

Fast FASTQ sample demultiplexing in Rust.

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

a pileup library that embraces the huge

Nam Genomes ⭐ 34

Detailed bioinformatics scripts and methods used in the NAM genome paper.

Biocommons.seqrepo ⭐ 34

non-redundant, compressed, journalled, file-based storage for biological sequences

🐳 Genomics Research Container Architecture

Awesome Bioinformatics ⭐ 33

A curated list of awesome Bioinformatics databases, softwares, libraries, toolboxes, pipelines, books, courses, tutorials and more.

Sscclust ⭐ 32

simpler single cell RNAseq data clustering

Read specialized NGS formats as data frames in R, Python, and more.

Bio Dockers ⭐ 32

🐳 Bio-dockers: dockerized bioinformatic tools

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

Nf Hack17 Tutorial ⭐ 31

Nextflow basic tutorial for newbie users

Orthogene ⭐ 31

🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

Wochenende ⭐ 30

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

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

A python package and a set of shell commands to handle GTF files

Mindthegap ⭐ 30

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

MiGA: Microbial Genomes Atlas

Minimum Information about any (X) Sequence” (MIxS) specification

Stratipy ⭐ 29

Graph regularized nonnegative matrix factorization (GNMF) in Python

The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline

Genomegraphs.jl ⭐ 29

A modern genomics framework for julia

Lightmotif ⭐ 28

A lightweight platform-accelerated library for biological motif scanning using position weight matrices.

Bac Genomics Scripts ⭐ 28

Collection of scripts for bacterial genomics

Workflows ⭐ 28

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Phylostratr ⭐ 28

An R framework for phylostratigraphy

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

Gcmodeller ⭐ 27

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Some useful python scripts for biologists

Cogclassifier ⭐ 27

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

Sevenbridges R ⭐ 27

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R

Create WDL documentation using Markdown.

Awesome Sequencing Tech Papers ⭐ 26

A collection of publications on comparison of high-throughput sequencing technologies.

Evaluating genome assemblies

Varsome Api Client Python ⭐ 26

Example client programs for Saphetor's VarSome annotation API

Busco_phylogenomics ⭐ 26

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

counts k-mers, written in rust

Genome-wide imputation pipeline

Smallrnaseq ⭐ 26

small rna-seq analysis package

Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

Compute N50/NG50 and auN/auNG

Tandem repeat expansion detection or genotyping from long-read alignments

Python bindings to UCSC BigWig and BigBed library

Chromoformer ⭐ 24

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

Application of pan-genome for population

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Order and orientation of complete bacterial genomes

Discover ⭐ 23

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

simple viewer for variant call format using htslib

Phylociraptor ⭐ 23

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Compare_genomes ⭐ 23

A comparative genomics workflow using Nextflow, conda, Julia and R

Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Guide Counter ⭐ 22

A better, faster way to count guides in CRISPR screens.

Sequencework ⭐ 22

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Docker containers for bioinformatics with a small footprint

Phage-Host Interaction Search Tool

Cmdbtools ⭐ 21

Command line tools for CMDB varaints browser

Sv Pipeline ⭐ 21

Pipeline for structural variation detection in cohorts

Genomeanalysismodule ⭐ 21

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Omicnavigator ⭐ 21

Open-Source Software for Omic Data Analysis and Visualization

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

Scaff10x ⭐ 20

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

a versatile toolkit for processing and analyzing diverse types of sequence data

Cgview Js ⭐ 20

CGView.js creates interactive circular and linear genome maps.

Gff3toembl ⭐ 20

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Mgcplotter ⭐ 20

Microbial Genome Circular plotting tool for comparative genomics using Circos

UFCG: Universal Fungal Core Genes

Predict plasmids from uncorrected long read data

Guix Genomics ⭐ 19

guix packages for bioinformatics software

Kgwasflow ⭐ 19

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

Companion ⭐ 19

Pipeline for automatic eukaryotic parasite annotation

Mosaicatcher Pipeline ⭐ 19

Integrated workflow for SV calling from single-cell Strand-seq data

Netsmooth ⭐ 18

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Hts Python ⭐ 18

pythonic wrapper for htslib

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.

R Interface to CoreArray Genomic Data Structure (GDS) Files (Development version only)

Wgs2ncbi ⭐ 18

Toolkit for preparing genomes for submission to NCBI

Clairs To ⭐ 18

ClairS-TO - a deep-learning method for tumor-only somatic SNV calling

PyPop: Python for Population Genomics

Find target sites for the miRNAs in genomic sequences

Python wrapper for wavefront alignment using WFA2-lib

Tools for producing pseudo-cgh of next-generation sequencing data

Genomics data re-analysis

Genomics_adventure ⭐ 17

Workshop on Genomics - Genomics Adventure

A tool to extract LOH blocks from VCF, BAM and FASTA data

ntHash implementation in Rust

Hicstuff ⭐ 17

Simple library/pipeline to generate and handle Hi-C data.

Related Searches

Python Bioinformatics (1,492)

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