herrinca

herrinca's Stars

• jlevy/the-art-of-command-line

  Master the command line, in one page

  153k2.8k25214.5k

• CamDavidsonPilon/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 ;)

  Language:Jupyter Notebook26.8k1.4k2457.9k

• jrjohansson/scientific-python-lectures

  Lectures on scientific computing with python, as IPython notebooks.

  Language:Jupyter Notebook3.5k308251.8k

• pydata/numexpr

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

  Language:Python2.2k59379210

• scverse/scanpy

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

  Language:Python1.9k511.7k597

• alex/nyt-2020-election-scraper

  Language:HTML1.8k36164289

• macs3-project/MACS

  MACS -- Model-based Analysis of ChIP-Seq

  Language:Python70249528268

• pachterlab/ffq

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

  Language:Python545135047

• broadinstitute/CellBender

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

  Language:Python2901031652

• bhargavchippada/forceatlas2

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

  Language:Python284103179

• dpeerlab/SEACells

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

  Language:Jupyter Notebook14566027

• hhcho/densvis

  Density-preserving data visualization tools den-SNE and densMAP

  Language:Python10981213

• YeoLab/single-cell-bioinformatics

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

  Language:Jupyter Notebook10016039

• YosefLab/Hotspot

  Language:Python8843114

• AllonMKlein/scrublet

  Detect doublets in single-cell RNA-seq data

  Language:Jupyter Notebook8514026

• Shians/Glimma

  Glimma R package

  Language:R5076610

• databio/awesome-atac-analysis

  Links to ATAC-seq analysis tools

  492006

• rasbt/numpy-intro-blogarticle-2020

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

  Language:Jupyter Notebook457016

• LTLA/SingleCellThoughts

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

  Language:TeX44926

• vals/Blog

  Language:Jupyter Notebook37259

• ManchesterBioinference/Scasat

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

  Language:Jupyter Notebook351056

• KenLauLab/pCreode

  An algorithm for mapping cell state transitions.

  Language:Jupyter Notebook2551513

• Iain530/force-directed-layout-algorithms

  Force directed layout algorithms for Python

  Language:Python21218

• daler/biomartpy

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

  Language:Python17343

• liuqivandy/scUnifrac

  Language:R12203

• LTLA/HVGDetection2018

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

  Language:TeX6301