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seandavi/awesome-single-cell

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

3.7K
Active
Databases
CLI Tools
#bioinformatics#single-cell#rna-seq

NAalytics/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273

An open-source project that provides experimental sequence information for the RNA components of the Moderna and Pfizer/BioNTech COVID-19 vaccines.

3.4K
Archived
File Storage
Databases
#covid-19#vaccines#rna-sequencing

scverse/scvi-tools

A Python library for deep probabilistic analysis of single-cell and spatial omics data.

1.6K
Active
Python
Computer Vision
Databases
Python
#single-cell-genomics#variational-autoencoder#deep-learning

theislab/single-cell-tutorial

A tutorial for best practices in single-cell RNA-seq analysis, useful for bioinformatics developers.

1.6K
Archived
Jupyter Notebook
Tutorials & Courses
ORMs & Query Builders
#bioinformatics#single-cell-analysis#rna-seq

griffithlab/rnaseq_tutorial

An educational resource for learning RNA-seq analysis including cloud computing, data formats, and visualization.

1.4K
Archived
R
Tutorials & Courses
R
#bioinformatics#rna-seq#data-analysis

nf-core/rnaseq

A Nextflow pipeline for RNA-seq analysis with extensive quality control features.

1.2K
Active
Nextflow
API Frameworks
Pipelines
Nextflow
#rna-seq#workflow#analysis

a-r-j/graphein

Graphein is a Python library for building and analyzing protein interaction graphs for drug discovery and computational biology.

1.2K
Active
Jupyter Notebook
Computer Vision
Databases
PyTorch
#bioinformatics#computational-biology#protein-structure

theislab/single-cell-best-practices

A comprehensive guide for best practices in single-cell RNA sequencing analysis.

1.2K
Active
Jupyter Notebook
Tutorials & Courses
Databases
#rna-seq#single-cell#tutorial

pachterlab/gget

gget is a Python library that enables efficient querying of genomic reference databases like NCBI, Ensembl, and UniProt.

1.1K
Active
Python
Databases
CLI Tools
#genomics#bioinformatics#data-access

PaddlePaddle/PaddleHelix

A bio-computing platform for large-scale representation learning and multi-task deep learning on molecular and biological data.

1.1K
Stable
Python
Machine Learning
Databases
Python
#biocomputing#representation-learning#deep-learning

crazyhottommy/RNA-seq-analysis

This GitHub repository contains notes and code for analyzing RNA-seq data using Python and Snakemake.

1.1K
Archived
Python
Databases
ETL & Pipelines
Python
#rna-seq#bioinformatics#data-analysis

bcbio/bcbio-nextgen

Validated, scalable, community-developed platform for variant calling, RNA-seq and small RNA analysis.

1.0K
Archived
Python
API Frameworks
Databases
Python
#bioinformatics#genomics#variant-calling

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