416 Open source projects that are alternatives of or similar to redbiom

JavaScript VisualizationTools

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

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…

Exact Tandem Repeat Finder (not a TRF replacement)

Core BioPerl 1.x code

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

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

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Strelka2 germline and somatic small variant caller

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

Randomly subsample sequencing reads to a specified coverage

Quickly search, compare, and analyze genomic and metagenomic data sets.

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

Method to optimally select samples for validation and resequencing

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Examples of using deep learning in Bioinformatics

UNCURL is a tool for single cell RNA-seq data analysis.

Qiita - A multi-omics databasing effort

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

Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.

🐣 locally query the ncbi taxonomy

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

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

🔬 Assemble large genomes using short reads

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Curated list of bioinformatics formats and publications

Fast & accurate alignment of barcoded short-reads

React component for Cytoscape.js network visualisations

(No maintenance) Detect gene fusion directly from raw fastq files

Compute N50/NG50 and auN/auNG

JAMP - Just Another Metabarcoding Pipeline

A curated list of resources for learning bioinformatics.

an implementation of NSGA-II in java

Mapping-Assisted Targeted-Assembly for Metagenomics

Data and analysis for the Splatter paper

Proof-of-concept seq-to-graph mapper and graph generator

A robust model for quantitative comparison of ChIP-Seq data sets.

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

Data intensive science for everyone.

Intuitive local web frontend for the BLAST bioinformatics tool

Aggregate results from bioinformatics analyses across many samples into a single report.

Phylogenetic trees in Julia

A plotly.js React component from Plotly 📈

Python package for graph neural networks in chemistry and biology

Python and C++ code for reading and writing genomics data.

WebGL Heatmap Viewer for Big Data and Bioinformatics

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

RAxML Next Generation: faster, easier-to-use and more flexible

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

A D library for computational biology and bioinformatics

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

DOM Text Based Multiple Sequence Alignment Library

BACNET is a Java based platform to develop website for multi-omics analysis

Examples using Clustergrammer2 to explore high-dimensional datasets.

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

GNparser normalises scientific names and extracts their semantic elements.

GCP Essentials for Bioinformatics Researchers