Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

python bioinformatics clustering gene-expression data-visualization dimensionality-reduction awesome-list data-integration atac-seq single-cell rna-seq-data scrna-seq-data cell-differentiation gene-expression-profiles analysis-pipeline spatial-transcriptomics cell-populations rna-seq-experiments cell-clusters

• Updated Nov 7, 2026

A language and runtime for distributed, incremental data processing in the cloud

language golang aws data-science runtime bioinformatics-pipeline scientific-computing cloud-computing analysis-pipeline

• Updated Oct 18, 2023
• Go

Assertive programming for R analysis pipelines

r assertions rstats predicate-functions r-package assertion-library assertion-methods analysis-pipeline peer-reviewed

• Updated Nov 12, 2026
• R

Automatic detection of defected solar panel modules

detection image-processing image-classification analysis-pipeline

• Updated Nov 15, 2017
• Python

Modules for processing extracellular electrophysiology data from Neuropixels probes

python3 electrophysiology spikes analysis-pipeline

• Updated Aug 18, 2024
• Python

eDNA metabarcoding pipeline

genomics metabarcoding environmental-dna analysis-pipeline

• Updated Sep 10, 2026
• Python

An alternative to MCMC for rapid analysis of models

python emulator model regression python3 model-analysis analysis-pipeline

• Updated Jun 28, 2021
• Python

A framework to build Software As A Service (SaaS) platforms for data analysis pipelines.

docker hadoop analysis-pipeline cloudgene cloudgene-saas

• Updated Apr 19, 2024
• Java

Enables data scientists to compose pipelines of analysis which consist of data manipulation, exploratory analysis & reporting, as well as modeling steps. Data scientists can use tools of their choice through an R interface, and compose interoperable pipelines between R, Spark, and Python.

python r spark analysis-pipeline interoperable-pipelines

• Updated Nov 23, 2020
• R

vSNP -- validate SNPs

bam-files snps pipeline genomics vcf phylogenetics snp wgs high-throughput-sequencing high tuberculosis whole-genome-sequencing analysis-pipeline mycobacterium-tuberculosis-complex brucella freebayes

• Updated Jun 24, 2026
• Python

The MaNGA Data Analysis Pipeline

astronomy spectroscopy analysis-pipeline

• Updated Jun 24, 2026
• Python

vSNP -- validate SNPs

bam-files snps pipeline genomics phylogenetics influenza wgs high-throughput-sequencing bwa-mem tuberculosis whole-genome-sequencing analysis-pipeline vcf-files mycobacterium-bovis mycobacterium-tuberculosis-complex mycobacterium-bovis-af2122 brucella freebayes sars-cov-2

• Updated Oct 28, 2026
• Python

Gradle tools to analyze bitcode of a Kotlin/Native project

gradle gradle-plugin bitcode analysis-pipeline kotlin-native gradle-kotlin-dsl kotlin-native-plugin bitcode-generation

• Updated Mar 11, 2024
• Kotlin

What people are tweeting about now, in your desired location? Live Streaming of Twitter Data to Spark and Tweet Analysis application on various trends Eg: Trending HashTags, Trending Mentions etc. Location based features supported.

twitter spark beginner-project pyspark spark-streaming spark-sql analysis-pipeline

• Updated Dec 26, 2018
• Python

Analysis pipeline capable of searching for dark compact objects in the Milky Way through astrometric lensing in real or mock Gaia DR4 data.

astronomy physics astrophysics gaia high-energy-physics gravitational-lensing telescope particle-physics dark-matter astrometry astroparticle-physics analysis-pipeline milky-way black-holes mock-data-generator neutron-stars dark-matter-halos primordial-black-holes phenomenology

• Updated Jun 20, 2023
• Jupyter Notebook

Lena is an architectural framework for data analysis

data-science data-analysis analysis-framework analysis-pipeline

• Updated Feb 18, 2026
• Python

Automated and friendly RNA-seq analysis (deprecated)

python docker automation quality-control rna-seq pipeline analysis portal kallisto alaska analysis-pipeline sleuth

• Updated May 21, 2019
• Python

AcetoScan - Automated pipeline for the unsupervised analysis of FTHFS amplicon sequencing

analysis-pipeline amplicon-sequencing fthfs acetogens acetobase

• Updated Aug 27, 2021
• Shell

PipiDABS: A Comprehensive and User-Friendly Pipeline for Downstream DNA Methylation Analysis of High-throughput Bisulfite Sequencing Data.

r dna-methylation analysis-pipeline bs-seq downstream-figures

• Updated Jul 3, 2022
• R

KREWS Scientific Data Pipeline Framework

kotlin workflows analysis-pipeline

• Updated Oct 25, 2023
• Kotlin