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awesome-single-cell

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

best-of-ml-python

🏆 A ranked list of awesome machine learning Python libraries. Updated weekly.

best-of-python

🏆 A ranked list of awesome Python open-source libraries and tools. Updated weekly.

bioc2016singlecell

Bioconductor workshop: Analysis of single-cell RNA-seq data with R and Bioconductor

brca_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".

capillary-tracking

cheatsheets

RStudio Cheat Sheets

depletion_probes

Script to design depletion probes

giotto

Spatial omics analysis toolbox

inseq_pipeline

julia

The Julia Programming Language

julia.jl

Curated decibans of Julia programming language.

machine-learning-made-easy-naive-bayes

pandas-cookbook

Recipes for using Python's pandas library

pandas_exercises

Practice your pandas skills!

probe_design

Scripts for picking optimal probes

prokseq

pythonidae

Curated decibans of scientific programming resources in Python.

r4ds

R for data science: a book

rlv3841_rnaseq

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

scanpy

Single-cell analysis in Python. Scales to >1M cells.

scrnaseq

setting_up_aws_ec2

Setting up

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

smorfinder

A command line tool to identify and annotate small proteins in microbial sequencing datasets.

sortn-seq

Smith et al., 2020: Inverse regulation of innate and CRISPR-Cas adaptive immunity selectively discriminates plasmids and phages in response to stress.

structural_variant_analysis

vinsilico.github.io

Webpage

viral_variant_calling_analysis

Variant Calling analysis of SARS CoV-2 genomics