398 Open source projects that are alternatives of or similar to Pysradb

Biostar Q&A

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

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

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

Global Biotic Interactions provides access to existing species interaction datasets

Streamlining SLAM-seq analysis with ultra-high sensitivity

Versatile open-source tool for microbiome analysis

An R package for reproducible and automated ADMIXTOOLS analyses

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

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

Workflow Description Language - Specification and Implementations

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)

Characterization of Germline variants

GRAph-based Finding of Individual Motif Occurrences

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

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

A collection of scripts and notes related to genomics and bioinformatics

The BridgeDb Library source code

A cross-platform command-line tool for executing jobs in parallel

GNparser normalises scientific names and extracts their semantic elements.

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

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

The next version of bwa-mem

Toolkit for preparing genomes for submission to NCBI

Single cell perturbation prediction

Computational Analysis of Novel Drug Opportunities

A modern genome browser built with JavaScript and HTML5.

The Ensembl Compara Perl API and SQL schema

Parser and database to index the terpene profile of different strains of Cannabis from online databases

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

Signal-level algorithms for MinION data

Haplotype VCF comparison tools

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A curated list of Cheminformatics libraries and software.

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

Official git repository for Biopython (originally converted from CVS)

A tutorial on methods of 16S analysis with QIIME 1

cython + htslib == fast VCF and BCF processing

Cutadapt removes adapter sequences from sequencing reads

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

nim wrapper for htslib for parsing genomics data files

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

Working with molecular structures in pandas DataFrames

Remote protein homology detection suite.

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

An ultrafast memory-efficient short read aligner

Java utilities for Bioinformatics

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

Antimicrobial Resistance Identification By Assembly

Bioinformatics one liners from Ming Tang

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

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

Bayesian haplotype-based mutation calling

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

SquiggleKit: A toolkit for manipulating nanopore signal data

A wrapper for the EnsEMBL REST API

React rerelease of MSAViewer