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awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

cancer_annotations

cre

excel report generation using data from bcbio variant2 germline pipeline

ctalign

ccfDNA Alignment pipeline with UMI calling. Snakemake workflow designed to align fastq reads, and call consensus on the barcoded reads tagged with UMI

data-sciene_notes-

📢 Ready to learn! you will learn 10 skills as data scientist:📚 Machine Learning, Deep Learning, Data Cleaning, EDA, Learn Python, Learn python packages such as Numpy, Pandas, Seaborn, Matplotlib, Plotly, Tensorfolw, Theano...., Linear Algebra, Big Data, Analysis Tools and solve some real problems such as predict house prices.

decart-2019-data-visualization

Materials for the DeCART 2019 Summer School Data Visualization Course

decart_advanced_python_2018

decart_linear_algebra_2019

dge_workshop_salmon_online

Copy for learning

evop2020

Python in 2 days for EVOP 2020 in Berlin

gatk-for-microbes

harvardcomputefest2021

hileup

horizontal pileup

intro-to-chipseq

Intro to ChIPseq using HPC

intro-to-chipseq-flipped

maskid

Masks the genotype variants sites in FastQ reads

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

notes_decart_bootcamp2

pfb2019

Programming for Biology 2019

pfb2019-walkthrough

This is a walkthrough of the PFB2018 course taught at CSHL.

preetida

Config files for my GitHub profile.

scanpy_usage

Scanpy use cases.

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"

sllobs-biostats

somalier

sample-swap checking directly on BAMs/CRAMs for cancer data

timeseries_organoid

scPrep/psuedotime with MAGIC and PHATE

trajectorynet

TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics

webinars

Training material based on webinar events