Rachel's repositories
Holtz-Lim_MotherTwinInfant_Virome_BacterialMicrobiome
Publication repository for twin/mom study (bacterial and viral).
Hecatomb-HTCF-Snake
Snakemake and associated files for Hecatomb on HTCF
16S_Analysis_Workshop
Code for 16S analysis workshop
191203_Baldridge_VLPtagging
Scripts for Larry's VLP Tagging project.
201113-Mouse-CRPS-Combined
Analyses of Lara Crock's combined mouse CRPS cohorts 1 and 2.
201129-Human-CRPS-Combined
Analysis of (5) combined human CRPS cohorts, inluding CRPS, HHC, and Biobank controls.
demux-htcf-snake
Snakemake for demultiplexing 16S sequencing files using QIIME1 on the cluster.
dirty-bbtools-viral-pipeline
The old, dirty bbtools pipeline up through assembly with IDBA_UD.
Friess_16S_Color_Picker
Color picker for 16S family-level community composition plot.
FundulidaePhylogenomics_RNAseq
Scripts and files associated with "Phylogenomic analysis of Fundulidae (Teleostei: Cyprinodontiformes) using RNA-sequencing Data"
hecatomb-eukVir-wrangling-r
Code for wrangling of eukaryotic viral data output from Hecatomb.
VirusVariantViewR-RShiny-Application
VirusVariantViewR RShiny application for viewing output from VirusVariantViewR-HTCF-Snake workflow.
KKing-TINMAN-Collaboration
Analysis of 16S and Metagenomic WGS data for TINMAN collaboration.
Phage-Pipeline-HTCF-Snake
Phage pipeline for HTCF.
pullseq
Utility program for extracting sequences from a fasta/fastq file
RachelRodgers
Config files for my GitHub profile.
Rumspringa-Coverge-Supplementary
Code for generation of supplementary variant information tables.
shared_R_scripts
Functions and variables for 16S microbiome analyses.
snakemake_helpers
Helper functions for Snakemake workflows
starter-web
Simple starting point website project based upon Initializr
STL5-phylogenetics
Phylogenetic tree construction of STL5 for HI Nat Micro Viral Complementation.
VirusVariantViewR
Snakemake workflow for detecting CR6 or CW3 viral variants.
VirusVariantViewR-Genomes
Code and data needed to generate reference genome information for the VirusVariantViewR workflow and R Shiny application.