358 Open source projects that are alternatives of or similar to bio-pipeline

Command line utility for manipulating Illumina-generated FastQ files.

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

An R framework for phylostratigraphy

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

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

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

🛠 Built a Example App of RealWorld with Nuxt & Composition API ⚗️

Spark VCF data source implementation for Dataframes

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.

A tool to plot significant regions of GWAS

Bioconductor package for management of multi-assay data

Learn interpretable computational phenotyping models from k-merized genomic data

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

An experiment to host a website with the content served over DNS.

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Interactive assembly and analysis of RAD-seq data sets

🐳 Bio-dockers: dockerized bioinformatic tools

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Identify phage regions in bacterial genomes for masking purposes

A package for designing activity-informed nucleic acid diagnostics for viruses.

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

The first C compiler written in Rust.. mostly unworking.

A fast, scalable, and accurate local ancestry method.

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Clustering scRNAseq by genotypes

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

mgatk: mitochondrial genome analysis toolkit

A digital playground for experimenting with creative coding and WebGL

pythonic wrapper for htslib

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

An experimental adaptive UI toolkit.

Multilocus sequence typing by blast using the schemes from PubMLST

A proof of concept of RNAseq pipeline

Addon compatible AI plugin for PocketMine-MP

Grammar of Scalable Linked Interactive Nucleotide Graphics

Documentation for Home Assistant Experimental UI: Lovelace

A modular annotation tool for genomic variants

Numerical Encoding for Human Genetic Variants

Tools for analyzing 10X Genomics data

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

R3-OS — Experimental static (μITRON-esque) RTOS for deeply embedded systems, testing the limit of Rust's const eval and generics

Named Yields for Ember Components

WebAssembly modules for genomics

Predict traffic flow with LSTM. For experimental purposes only, unsupported!

Transcripts annotation and GO enrichment Fisher tests

Predict AMPs in (meta)genomes and peptides

No description or website provided.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

Resource of human chromosome schematics & images

Chanjo provides a better way to analyze coverage data in clinical sequencing.

Environmental DNA metabarcoding taxonomic identification

OnceBuilder - managment tool, mange projects, templates, plugins in one place.

willdady.github.io/swirlr-wasm/

find large indels (in the blind spot between GATK/freebayes and SV callers)