425 Open source projects that are alternatives of or similar to Awesome Cancer Variant Databases

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

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

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.

R package for analyzing single-cell RNA-seq data

Per-base per-nucleotide depth analysis

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

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Randomly subsample sequencing reads to a specified coverage

Assembling the cause of phenotypes and genotypes from NGS data

A powerful open source data warehouse system

Stacked Denoising AutoEncoder based on TensorFlow

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

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

SortMeRNA: next-generation sequence filtering and alignment tool

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

A versatile pairwise aligner for genomic and spliced nucleotide sequences

An open-access bioinformatics text

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

Unsupervised domain adaptation method for relation extraction

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

Fast and flexible ORF finder

microsatellite instability detection using tumor only or paired tumor-normal data

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

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

Method to optimally select samples for validation and resequencing

Rapid large-scale prokaryote pan genome analysis

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

🐣 locally query the ncbi taxonomy

Compute N50/NG50 and auN/auNG

A collection of scripts and notes related to genomics and bioinformatics

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

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

WebGL Heatmap Viewer for Big Data and Bioinformatics

parallel fastq-dump wrapper

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

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

A package for designing compact and comprehensive capture probe sets.

Inference of ploidy and heterozygosity structure using whole genome sequencing data

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Fast & accurate alignment of barcoded short-reads

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

GenomeTools genome analysis system.

Read and write FASTQ and FASTA efficiently from Python

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

Fast hash function for DNA sequences

Antimicrobial Resistance Identification By Assembly

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

JAMP - Just Another Metabarcoding Pipeline

Simple pure Python SAM parser and objects for working with SAM records

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

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

an implementation of NSGA-II in java

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

Intuitive local web frontend for the BLAST bioinformatics tool

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

Python for Bioinformatics

The sources of the openSNP website

A tool to circularize genome assemblies

Genome inference from a population reference graph