412 Open source projects that are alternatives of or similar to CATT

GWAS summary statistics files QC tool

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data

Genomics data visualization in Python by using matplotlib.

MView extracts and reformats the results of a sequence database search or multiple alignment.

Improving genome bins through the combination of different binning programs

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Classify sequencing reads using MinHash.

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

Version 5 of the CAFE phylogenetics software

API for linked biological knowledge

A permissively licensed library designed to replace Illumina's Experiment Manager

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

Ploidy agnostic phasing pipeline and algorithm

📊 Codon usage tables in code-friendly format + Python bindings

A curated list of resources for machine learning for small-molecule drug discovery

Single Cell Analysis Pipelines

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Genomics using open source tools, running on GCP or AWS

Golang for Bioinformatics

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

Toolkit for preparing genomes for submission to NCBI

Feature extraction algorithm for genomic data

A Kotlin DSL and library to create and plot RNA 2D structures

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

An R package for reproducible and automated ADMIXTOOLS analyses

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

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

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

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Read and write FASTQ and FASTA efficiently from Python

GRAph-based Finding of Individual Motif Occurrences

WebGL Heatmap Viewer for Big Data and Bioinformatics

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Fast hash function for DNA sequences

The BridgeDb Library source code

Method to optimally select samples for validation and resequencing

GNparser normalises scientific names and extracts their semantic elements.

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

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

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

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

Computational Analysis of Novel Drug Opportunities

Compute N50/NG50 and auN/auNG

The Ensembl Compara Perl API and SQL schema

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

A faster lmm for GWAS. Supports GPU backend.

A simple command-line tool to download data from Joint Genome Institute databases

A package for designing compact and comprehensive capture probe sets.

Open source Java library for computational proteomics

A modular annotation tool for genomic variants

A Python platform for Structural Bioinformatics

Mulled - Automatized Containerized Software Repository