761 Open source projects that are alternatives of or similar to slamdunk

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Feature extraction algorithm for genomic data

🚦 Run Picard on BAM files and collate 90 metrics into one file.

A library to build and execute typed scientific workflows

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

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

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

The Microbiome Interpretable Temporal Rule Engine

Aggregate results from bioinformatics analyses across many samples into a single report.

Fitness landscape exploration sandbox for biological sequence design.

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

a token based matrix registration api

A faster lmm for GWAS. Supports GPU backend.

An API Wrapper for Vestaboards written in Python

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

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)

command-line script to download headspace packs, singles, everyday meditation and other sessions. You could also download all packs at once

Genomics using open source tools, running on GCP or AWS

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

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

Single Cell Analysis Pipelines

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

A blazingly fast online judge/ autograder ⚖️ built with Python and the Django framework to test cases against your solution. Check out the sponsor links and help fund DomeCode.

Python project template/scaffold and best practices

cp-tool is an auto generator for solved problems at different online judges.

No description or website provided.

The Ensembl Compara Perl API and SQL schema

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

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

Classify sequencing reads using MinHash.

Porting DESeq2 and DEXSeq into python via rpy2

The BridgeDb Library source code

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

Asynchronous Library made using Python and aiohttp to get proxies from multiple services!

Some bits of javascript to transcribe scanned pages using PageXML

GNparser normalises scientific names and extracts their semantic elements.

RNA-seq analysis pipeline for detection gene-fusions

A command line tool that creates bibtex entries for IETF RFCs and Internet Drafts.

Summer school course materials collection

Crawl sites for RSS, Atom, and JSON feeds.

Reference-based transcript discovery from long RNA read

Improving genome bins through the combination of different binning programs

A Go package for engineering organisms.

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

Clustering scRNAseq by genotypes

GRAph-based Finding of Individual Motif Occurrences

Query network abuse contacts for a given ip address on abuse-contacts.abusix.zone

Toolkit for preparing genomes for submission to NCBI

A real-time transcription project using React and socketio

Translates standard alphabet based text to Grade 2 Braille and back.

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

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

FEELnc : FlExible Extraction of LncRNA

The 134,000+ words and their pronunciations in the CMU pronouncing dictionary

A pipeline for the computational evaluation of RNA-Seq data

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

Easy home automation with MQTT and/or openHAB

🐍 Twitter Accounts Activity API Client Library for Python

Interactive Differential Expression AnaLysis - DE made accessible and reproducible