401 Open source projects that are alternatives of or similar to awesome-bioinformatics-formats

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Rapid determination of appropriate reference genomes.

A library to build and execute typed scientific workflows

Per-base per-nucleotide depth analysis

A Python platform for Structural Bioinformatics

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

Stacked Denoising AutoEncoder based on TensorFlow

Examples using Clustergrammer2 to explore high-dimensional datasets.

3D printed sculpture of a DNA molecule, showing my own genome

React rerelease of MSAViewer

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

Genomics data visualization in Python by using matplotlib.

Predict plasmids from uncorrected long read data

Assembling the cause of phenotypes and genotypes from NGS data

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

GWAS summary statistics files QC tool

A fast 23andMe genome text file parser, now superseded by arv

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

Fast motif matching in R

Bystro genetic analysis (annotation, filtering, statistics)

VirNet: A deep attention model for viral reads identification

Mulled - Automatized Containerized Software Repository

Genotyping of segregating mobile elements insertions

Read DNA sequences from colourful Microsoft Word documents

Compute N50/NG50 and auN/auNG

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

Fast alignment and preprocessing of chromatin profiles

Project metadata manager for PEPs in Python

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Introduction to the Unix Shell for biologists

A computational library for learning and evaluating biological knowledge graph embeddings

No description or website provided.

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Mapping-Assisted Targeted-Assembly for Metagenomics

Provide R access to the NCI Genomic Data Commons portal.

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Useful bioinformatic scripts

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

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

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

An open-access bioinformatics text

exploratory and interactive microbiome analyses based on heatmaps

Unsupervised domain adaptation method for relation extraction

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

Fast and flexible ORF finder

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

📊 Identify cell types and pathways affected by genetic risk loci.

Method to optimally select samples for validation and resequencing

A curated list of awesome bioinformatics software.

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

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

Earl Grey: A fully automated TE curation and annotation pipeline

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

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

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