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

exploratory and interactive microbiome analyses based on heatmaps

A fast and scalable phylogenetic tree viewer for microbiome data analysis

The Microbiome Interpretable Temporal Rule Engine

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

Schloss Lab Tools for Reproducible Microbiome Research 💩

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

Introduction to the Unix Shell for biologists

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

The Ontology for Biomedical Investigations

Earl Grey: A fully automated TE curation and annotation pipeline

Fast motif matching in R

VirNet: A deep attention model for viral reads identification

No description or website provided.

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

MMseqs2 app to run on your workstation or servers

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

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

A library to build and execute typed scientific workflows

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

A fast 23andMe genome text file parser, now superseded by arv

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

A curated list of awesome bioinformatics software.

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.

micca - MICrobial Community Analysis

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

Read DNA sequences from colourful Microsoft Word documents

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

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

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

A simplified pipeline for ctDNA sequencing data analysis

R package for microbiome biomarker discovery

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

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…

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

Qiita - A multi-omics databasing effort

Curated list of bioinformatics formats and publications

Mapping-Assisted Targeted-Assembly for Metagenomics

Phylogenetic trees in Julia

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

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

Fast alignment and preprocessing of chromatin profiles

WebLogo 3: Sequence Logos redrawn

Compare different differential abundance and expression methods

No description or website provided.

React rerelease of MSAViewer

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.

Genotyping of segregating mobile elements insertions

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

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

Predict plasmids from uncorrected long read data

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

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.

Project metadata manager for PEPs in Python

Per-base per-nucleotide depth analysis

De novo assembly based variant calling pipeline for Illumina short reads

Genomics data visualization in Python by using matplotlib.

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

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