Most popular bioinformatics repositories and open source projects

Perl-for-Bioinformatics

An attempt to help anyone interested in using Perl for Bioinformatics

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hotsub

Command line tool to run batch jobs concurrently with ETL framework on...

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PrimerMiner

R mased batch sequence downloader, with primer development and in sili...

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transabyss

de novo assembly of RNA-seq data using ABySS

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genipe

Genome-wide imputation pipeline

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ema

Fast & accurate alignment of barcoded short-reads

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RNAseq_titration_results

Cross-platform normalization enables machine learning model training o...

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basic

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Bio3DView.jl

A Julia package to view macromolecular structures in the REPL, in a Ju...

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spacepharer

SpacePHARER CRISPR Spacer Phage-Host pAiRs findER

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teaching

scripts and notes for learning

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contact_map

Contact map analysis for biomolecules; based on MDTraj

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fastenloc

Colocalization analysis of genetic association signals

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pafpy

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

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phylostratr

An R framework for phylostratigraphy

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mokapot

Fast and flexible semi-supervised learning for peptide detection in Py...

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bisqueUCSB

An ML Platform for storing, analyzing, and visualizing your data all i...

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Tome

A machine learning model for the prediction of optimal growth temperat...

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rustybam

bioinformatics toolkit in rust

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Genome-annotation-pipeline

Genome annotation pipeline

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ska.rust

Split k-mer analysis – version 2

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GenEra

genEra is an easy-to-use, low-dependency command-line tool that estima...

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safepy

Python implementation of Spatial Analysis of Functional Enrichment (SA...

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lsf

Snakemake profile for running jobs on an LSF cluster

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cpgtools

Python package to analyze DNA methylation data

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propy3

A Python 3 version of the protein descriptor package propy

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self-study

My Self-Study Room: keep tidy and lightweight

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cgview

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

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BookChapter-RNA-Seq-Analyses

Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq an...

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Pipelines.jl

A lightweight and powerful Julia package for computational pipelines a...

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aws-for-bioinformatics

AWS for Bioinformatics Researchers

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TAPE

Deep learning-based tissue compositions and cell-type-specific gene ex...

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lsaBGC

lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

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SLAT

Spatially-Linked Alignment Tool

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gtdb-taxdump

GTDB taxonomy taxdump files with trackable TaxIds

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fastheatmap

Super high performance interactive heatmap software

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ngstools

My own tools code for NGS data analysis (Next Generation Sequencing)

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orchid

A novel management, annotation, and machine learning framework for ana...

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vue-cwl

Visualizer of CWL (Common Workflow Language) workflows for Vue

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dna_lstm

LSTM for binary DNA sequence classification

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biozsh

the z in bioinformatics

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virnet

VirNet: A deep attention model for viral reads identification

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SOAPdenovo-Trans

SOAPdenovo-Trans, a de novo transcriptome assembler designed specifica...

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BioCore.jl

Core types and interfaces for BioJulia packages

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TADLib

A Library to Explore Chromatin Interaction Patterns for Topologically...

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GATK4_Best_Practice

GATK4 Best Practice Nextflow Pipeline

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READemption

A pipeline for the computational evaluation of RNA-Seq data

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panphlan

PanPhlAn is a strain-level metagenomic profiling tool for identifying...

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candis

:ribbon: A data mining suite for gene expression data.

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libmol

Single Page Web Application for displaying and studying molecular mode...

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