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2018_scworkshop

adapters

Adapters for trimming

ai-for-medicine

Notebooks from DeepLearning.AI's AI for Medicine course

aligner

Aligner Comparison

annotationtutorial

bayesian-first-aid-rpackage

Inside every classical test there is a Bayesian model trying to get out.

beautiful-jekyll

✨ Build a beautiful and simple website in literally minutes. Demo at https://beautifuljekyll.com

bedtools2

bedtools - the swiss army knife for genome arithmetic

bioinfscripts

Bioinformatics scripts produced over the course of my work. Now maintained on GitLab.

blog

bootstrap-subsampling

Scripts used to carry out bootstrap subsampling

casper

covid-19_lung_atlas

covid-engine

COVID-engine is a pipeline method for PBMC-based gene signatures for systems-level analysis

covid19_respiratory_microbiome

Code accompanying the manuscript "Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host"

customized-upset-plots

Make customized upset plots: from raw data to plots

data-science-seminar

Topics In Data Science and Bioinformatics

differential-dropout-analysis

Differential dropout analysis captures biological variation in single-cell RNA sequencing data

doublet-detection-benchmark

Benchmarking computational doublet-detection methods for single-cell RNA sequencing data

dr-structure-preservation

A quantitative framework for evaluating data structure preservation by dimensionality reduction techniques

drop_it_like_its_hot_r

Compilation of R heatmap functions.

examples

A comparison of the dimensionality reduction results using t-SNE, UMAP, PCA, and TriMap

excelerate-scrnaseq

Single RNA-seq data analysis with R (Finland, May, 2019)

f1000imputation

fcs_tutorial

A tutorial for dealing with FCS files in both Python and R. Includes instruction for arcsinh transform, selecting relevant markers, etc.

fungeno2019

geoquery-scripts

Scripts using GEOquery package to fetch expression matrices and phenotypic data associated with GSE datasets

getsra

wrapper bash scripts to download fastq files from SRR

goview

A function package to view the results from gProfileR

igdiscover

Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads