432 Open source projects that are alternatives of or similar to biskit

code for reading and processing Allen Institute for Brain Science data

Fast hash function for DNA sequences

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

The BridgeDb Library source code

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

GRAph-based Finding of Individual Motif Occurrences

Stylo est un éditeur de textes pour articles scientifiques en sciences humaines et sociales.

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

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

Computational Analysis of Novel Drug Opportunities

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

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

An R package for reproducible and automated ADMIXTOOLS analyses

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

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

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

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

GNparser normalises scientific names and extracts their semantic elements.

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

Toolkit for preparing genomes for submission to NCBI

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

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

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

A faster lmm for GWAS. Supports GPU backend.

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

🎯 Human transcription factor target genes.

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

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

Improving genome bins through the combination of different binning programs

Ploidy agnostic phasing pipeline and algorithm

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

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

Classify sequencing reads using MinHash.

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

Single Cell Analysis Pipelines

WebGL Heatmap Viewer for Big Data and Bioinformatics

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

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).

Mulled - Automatized Containerized Software Repository

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

API for linked biological knowledge

Genomics using open source tools, running on GCP or AWS

Version 5 of the CAFE phylogenetics software

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

Golang for Bioinformatics

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

Compute N50/NG50 and auN/auNG

Scientific Computing for Chemists text for teaching basic computing skills to chemistry students using Python, Jupyter notebooks, and the SciPy stack. This text makes use of a variety of packages including NumPy, SciPy, matplotlib, pandas, seaborn, NMRglue, SymPy, scikit-image, and scikit-learn.

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

The Ensembl Compara Perl API and SQL schema

Feature extraction algorithm for genomic data

Hackerfleet Operating System

Open source Java library for computational proteomics

Method to optimally select samples for validation and resequencing

ERT—Ensemble based Reservoir Tool—is a tool to run ensemble based on reservoir models. ERT was originally devised as tool to do model updating (history matching) with the EnKF method, now the primary method for model updating is the Ensemble Smoother (ES).

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

A package for designing compact and comprehensive capture probe sets.