Pinned Repositories
Assemblathon
Code that was used in the Assemblathon 1 and 2 projects
CEGMA_v2
The final version 2 release of our software to detect core genes in eukaryotic genomes
Centromere_repeat_paper
Code used to generate data for our analysis of centromeric repeats
imeter
2022 reboot of IME project
Perl_utils
Miscellaneous Perl scripts and modules used by people in the Korf lab
Rosalind
Solutions to Rosalind problems
setup
How to set up your work environment
SNAP
Gene prediction software
StochHMM
A Hidden Markov Model Application and C++ Library for Rapid and Flexible Development of HMMs
unix_and_perl
The Korf Lab's Repositories
KorfLab/CEGMA_v2
The final version 2 release of our software to detect core genes in eukaryotic genomes
KorfLab/Assemblathon
Code that was used in the Assemblathon 1 and 2 projects
KorfLab/LearnGit
Let's Learn Git
KorfLab/Perl_utils
Miscellaneous Perl scripts and modules used by people in the Korf lab
KorfLab/CEGMA_v3
CEGMA (Core Eukaryotic Genes Mapping Approach), for building a highly reliable set of gene annotations in the absence of experimental data.
KorfLab/Centromere_repeat_paper
Code used to generate data for our analysis of centromeric repeats
KorfLab/FRAG_project
To contain code and data files for the Fragmentation project, investigating shattered chromosome phenotypes in Arabidopsis thaliana
KorfLab/Rosalind
Solutions to Rosalind problems
KorfLab/Suecica
Scritps written for research on A. suecica for Luca Comai's lab
KorfLab/unix_and_perl
KorfLab/DupHMM
An easy to use hidden Markov model-based copy number variant identifier
KorfLab/IME
A new code base for the IME project.
KorfLab/julie
Bioinformatics experiments with Julia
KorfLab/Milk-DNase-Seq-Project
Analysis of milk DNase-Seq data in mouse and human
KorfLab/Ploidamatic
StochHMM-based decoder for detecting copy number from alignments
KorfLab/Sickle
KorfLab/C9
KorfLab/GC_cluster_manual
Documentation about how to use the UC Davis Genome Center compute cluster
KorfLab/Genesmith
Gene finder mixing genomic and protein information
KorfLab/HMMstar-perl
Perl modules for HMMs (training mostly)
KorfLab/languages
An exploration of different languages
KorfLab/Macaque
Scripts written for research on Rhesus macaque for Satya Dandekar's lab
KorfLab/Mermade
Bind-n-Seq processing
KorfLab/mmdecoder
KorfLab/specDB
Database of protein NMR spectra