herrinca

numpy-intro-blogarticle-2020

Jupyter Notebook for the "Scientific Computing in Python: Introduction to NumPy and Matplotlib" blog article

pCreode

An algorithm for mapping cell state transitions.

SEACells

SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

ffq

A tool to find sequencing data and metadata from public databases.

densvis

Density-preserving data visualization tools den-SNE and densMAP

Hotspot

nyt-2020-election-scraper

Glimma

Glimma R package

awesome-atac-analysis

Links to ATAC-seq analysis tools

scrublet

Detect doublets in single-cell RNA-seq data

SingleCellThoughts

Assorted thoughts, explanations and justifications for code in the scran package and the simpleSingleCell workflow.

CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

biomartpy

Simple interface to BioMart (Python -> rpy2 -> R/BioConductor's biomaRt)

MACS

MACS -- Model-based Analysis of ChIP-Seq

Scasat

Scasat is a single cell ATAC-seq preprocessing and analysis pipeline

scanpy

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

HVGDetection2018

Justification for the variance modelling and HVG detection methods in scran.

the-art-of-command-line

Master the command line, in one page

single-cell-bioinformatics

Course material in notebook format for learning about single cell bioinformatics methods

forceatlas2

Fastest Gephi's ForceAtlas2 graph layout algorithm implemented for Python and NetworkX

force-directed-layout-algorithms

Force directed layout algorithms for Python

numexpr

Fast numerical array expression evaluator for Python, NumPy, Pandas, PyTables and more

scUnifrac

Probabilistic-Programming-and-Bayesian-Methods-for-Hackers

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

scientific-python-lectures

Lectures on scientific computing with python, as IPython notebooks.

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