hkim's repositories
bggn213_F20
Fall 2020 BGGN-213 class website
bggn213_W21
Winter 2021 BGGN-213 class website
bimm143_F20
Undergraduate Laboratory Course in Bioinformatics Fall 2020
bimm143_S21
Undergraduate Laboratory Course in Bioinformatics Spring 2021
BRCA-LRseq-pipeline
Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.
CGP-Somatic-Docker
Dockerised and simplified version of SeqWare-CGP-SomaticCore
classweb
Template for class websites
configs
Config files used to define parameters specific to compute environments at different Institutions
coursework
Help Manage Barry's Courses
curriculum_contribution
guidelines for contributing to fredhutch.io courses
epihet
EpiHet
fingerprint_maps
Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of functional genomic data.
git_github_intro
three class intro to git: git workflow in desktop app, GitHub, command line git
gm-cells-chiadrop
Scripts to reproduce results presented in "Single-molecule mapping reveals the dynamics of chromatin folding in the human genome"
HDA2020
High Dimensional Data Analysis
ml4calibrated450k
This is a companion repository for the article "Comparative analysis of machine learning classifiers and calibration algorithms for estimating class probabilities for personalized cancer diagnostics on DNA methylation microarray data"
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
RoseTTAFold
This package contains deep learning models and related scripts for RoseTTAFold
signature.tools.lib
R package containing useful functions for mutational signature analysis
SigProfilerSimulator
SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
telomeasure
Telomeasure estimates average telomere length from whole genome sequencing (WGS) BAM files.
valibam
Minimal nextflow pipeline to check integrity of BAM files with various tools and to generate the checksum (md5) of each files.