398 Open source projects that are alternatives of or similar to Single Cell Pseudotime

Syntax highlighting for computational biology

R package for analyzing single-cell RNA-seq data

A genome browser that shows long reads and complex variants better

Annotated data.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

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

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

A curated list of resources for learning bioinformatics.

parallel fastq-dump wrapper

Toolset for SV simulation, comparison and filtering

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

nim wrapper for htslib for parsing genomics data files

Python package for graph neural networks in chemistry and biology

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

React component for Cytoscape.js network visualisations

The sources of the openSNP website

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

Next generation sequencing reads de novo assembler.

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

Package for fetching metadata and downloading data from SRA/ENA/GEO

Deep learning infrastructure for bioinformatics

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

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

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

Reads simulator

Cuneiform distributed programming language

Fast multi-line FASTA/Q reader in several programming languages

A powerful open source data warehouse system

Curated (meta)list of resources for Biology.

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

A repository for setting up a RNAseq workflow

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Tools for working with genomic and high throughput sequencing data.

Remote protein homology detection suite.

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Bioconductor cheat sheet

🔬 BEDOPS: high-performance genomic feature operations

BioGrakn Knowledge Graph

GenomeTools genome analysis system.

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Protein Graph Library

A curated list of bioinformatics bench-marking papers and resources.

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Python for Bioinformatics

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

An ultrafast memory-efficient short read aligner

Bayesian haplotype-based mutation calling

Ten Quick Tips for Deep Learning in Biology

A comprehensive library for computational molecular biology

code for reading and processing Allen Institute for Brain Science data

Genome assembly evaluation tool

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

Examples of using deep learning in Bioinformatics

🔬 Assemble large genomes using short reads

Intuitive local web frontend for the BLAST bioinformatics tool

Rapid large-scale prokaryote pan genome analysis