Repositories list

• CHTC_RNAseq_RSEM

  Public
  RNAseq pipeline that uses STAR and RSEM to produce normalized counts. Condor scripts written to be used on CHTC servers with Docker Containers.

  Shell

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• CHTC_RNAseq_HTSeqCounts

  Public
  Updated versions of condor scripts for work on CHTC for RNAseq using Docker containers.

  Python

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• RGAPepPipe_CHTC

  Public
  Updated versions of condor scripts for work on CHTC for RGAPepPipe using Docker containers

  Python

  •3•1•0•0•Updated Oct 16, 2024Oct 16, 2024

• nano-RGA

  Public
  SNP calling for Nanopore data

  Python

  •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

• cv-pangraph

  Public
  pangraph analysis of nanopore sequenced colony variants

  Shell

  •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• Mtb_COBS

  Public
  Scripts to estimate frequency of mutations identified in Contingencies in biofilm adaptation of Mycobacterium tuberculosis (Kernien & Youngblom et al. 2024) in a global dataset of M.tb genomes using a previously described method (Smith et al. 2022).

  Python

  •0•0•0•0•Updated May 21, 2024May 21, 2024

• poolER

  Public
  analysis of evolve and re-sequence populations

  Python

  •2•0•0•0•Updated May 21, 2024May 21, 2024

• selection-stats

  Public
  Python

  •1•0•0•0•Updated Mar 25, 2024Mar 25, 2024

• mtb_ExpEvo_RNA

  Public
  Scripts for analysis and figures associated with the following publication: Adaptation of the Mycobacterium tuberculosis transcriptome to biofilm growth

  R

  •

  MIT License

  •1•0•0•0•Updated Dec 20, 2023Dec 20, 2023

• sapro_genomics

  Public
  R

  •1•0•0•0•Updated May 29, 2023May 29, 2023

• scripts

  Public
  Misc scripts not yet associated with a project/publication

  Python

  •1•0•0•0•Updated May 26, 2023May 26, 2023

• Evolution_of_the_GGI

  Public
  Scripts for analysis and figures associated with the following publication: "The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae"

  R

  •

  MIT License

  •1•0•0•0•Updated May 26, 2023May 26, 2023

• RNAseq

  Public
  scripts (condor, submit & shell) for processing and analysis of bacterial RNAseq

  Python

  •1•0•0•0•Updated May 26, 2023May 26, 2023

• cdiff_gwas

  Public
  Shell

  •1•0•0•0•Updated May 26, 2023May 26, 2023

• RGAPepPipe_MAY

  Public
  Updated versions of condor scripts for RGAPepPipe

  Python

  •3•0•0•0•Updated May 24, 2023May 24, 2023

• VGS_GWAS

  Public
  Scripts for analysis and figures associated with the following publication: "Comparative Genomics of Streptococcus oralis Identifies Large Scale Homologous Recombination and a Genetic Variant Associated with Infection"

  Python

  •

  MIT License

  •1•0•0•0•Updated Apr 22, 2023Apr 22, 2023

• mtb_ExpEvo

  Public
  Scripts for analysis and figures associated with the following publication: "Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis"

  Python

  •

  MIT License

  •1•0•0•0•Updated Jun 14, 2022Jun 14, 2022

• RGAPepPipe

  Public
  Reference Guided Assembly Pepperell Lab Pipeline

  Python

  •

  MIT License

  •2•1•0•0•Updated Mar 30, 2021Mar 30, 2021

• blasto

  Public
  Scripts pertaining to the blastomycosis project

  R

  •0•1•0•0•Updated Sep 8, 2018Sep 8, 2018

• alignmentQC

  Public
  QC scripts for alignments

  Python

  •

  MIT License

  •1•1•0•0•Updated Jun 26, 2018Jun 26, 2018

• saprophyticus

  Public
  Data and scripts associated with S. saprophyticus selection project

  PostScript

  •

  MIT License

  •0•0•0•0•Updated Nov 7, 2017Nov 7, 2017

• mtbDrugResistance

  Public
  The population genetics of drug resistance in Mycobacterium tuberculosis

  HTML

  •2•0•0•0•Updated Aug 7, 2017Aug 7, 2017

• MtbLineageClassifier

  Public
  Classifies lineage of Mtb based on RGA to H37Rv

  Python

  •0•1•0•0•Updated Jan 27, 2017Jan 27, 2017

• in-vitro

  Public
  R

  •0•0•0•0•Updated Dec 15, 2016Dec 15, 2016

• Phylogeography

  Public
  HTML

  •0•2•1•0•Updated Dec 13, 2016Dec 13, 2016

• submitFiles

  Public
  Condor submit files (and executable where applicable)

  Python

  •0•1•0•0•Updated Jul 12, 2016Jul 12, 2016

• Functional_Enrichment

  Public
  Scripts for functional enrichment analysis

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 17, 2016Feb 17, 2016

• WH-BH

  Public
  Within-host, Between-host Project

  Python

  •0•0•0•0•Updated Jul 2, 2015Jul 2, 2015