KR's starred repositories
bulk-rnaseq-analysis
A complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression analysis using DESeq2, using example data from Guo et al. 2019.
IsoformSwitchAnalyzeR
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
Visium_SPG_AD
Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.
template_project
Template project following the guidelines from https://lcolladotor.github.io/bioc_team_ds/organizing-your-work.html#.YzL43uzMKX0
modern-bayes
Modern Bayesian statistics, STA 360/602, Duke University, Department of Statistical Science
minimal_nextflow_samplesheet_example
A minimal RNAseq workflow, written in Nextflow, an example of using a samplesheet for metadata.
stat_rethinking_2022
Statistical Rethinking course winter 2022
ltc_palettes
"ltc_palettes: Tailored for data visualization enthusiasts, ltc_palettes is an R package that offers a curated collection of color palettes. Crafted to enhance clarity and impact, these palettes ensure that your visual representations not only communicate data effectively but also aesthetically
coding_exercise_TCGA_infiltration
coding exercise using TCGA immune infiltration data
neat-genreads
NEAT read simulation tools
TAPS-pipeline
Codes for processing of methylation data generated using the TAPS method
Scientific-Inkscape
Scientific Inkscape: Inkscape extensions for figure resizing and editing
squigulator
a tool for simulating nanopore raw signal data
molecular-cfDNA-fragmentomics
An et al. Nature Communications 2023
Fragmentomics_GenomBiol
Pipeline to replicate Katsman et. al fragmentomics results
comp-genomics-class
Code and examples for JHU Computational Genomics class
RNA-seq-analysis
RNAseq analysis notes from Ming Tang
BI-BE-CS-183-2023
Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
cookiecutter
A cross-platform command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, C projects.
wargame-nexus
A sorted and updated list of security wargame sites.
lowlevelprogramming-university
How to be low-level programmer