Pinned Repositories
16S_QIIME2
Snakemake based 16S QIIME2 pipeline
adonisplus
dnabc
Identify DNA barcodes in high-throughput sequencing data files
mirix
Quantify the susceptibility of a bacterial community to an antibiotic.
primertrim
Trim primers from reads
seqBackup
ShotgunPipeline
unassigner
Type strain identification for 16S reads
ZIBR
Zero-Inflated Beta Random Effect model
ZIR
Zero-Inflated (Wilcoxon and Kruskal–Wallis) Rank Test
PennChopMicrobiomeProgram's Repositories
PennChopMicrobiomeProgram/ZIBR
Zero-Inflated Beta Random Effect model
PennChopMicrobiomeProgram/ZIR
Zero-Inflated (Wilcoxon and Kruskal–Wallis) Rank Test
PennChopMicrobiomeProgram/unassigner
Type strain identification for 16S reads
PennChopMicrobiomeProgram/adonisplus
PennChopMicrobiomeProgram/mirix
Quantify the susceptibility of a bacterial community to an antibiotic.
PennChopMicrobiomeProgram/16S_QIIME2
Snakemake based 16S QIIME2 pipeline
PennChopMicrobiomeProgram/decontam
PennChopMicrobiomeProgram/illqc
Process shotgun metagenomic DNA data for quality
PennChopMicrobiomeProgram/primertrim
Trim primers from reads
PennChopMicrobiomeProgram/SampleRegistry
Web application to keep track of samples sequenced
PennChopMicrobiomeProgram/seqBackup
PennChopMicrobiomeProgram/ShotgunPipeline
PennChopMicrobiomeProgram/CHOP_metadata_checker
PennChopMicrobiomeProgram/dnabc
Identify DNA barcodes in high-throughput sequencing data files
PennChopMicrobiomeProgram/bacphene
Imports Bacterial Phenotype Data Into R
PennChopMicrobiomeProgram/FARMM
Code used to generate the results and figures for the FARMM study.
PennChopMicrobiomeProgram/gutsandcages
A package to calculate power for mouse and rat experimental design
PennChopMicrobiomeProgram/ITS_PIPITS_BROCC
PennChopMicrobiomeProgram/microflowseq
PennChopMicrobiomeProgram/PathwayAbundanceFinder
A short wrapper for finding presence/absence/abundance of pathways from metagenomic data.
PennChopMicrobiomeProgram/PCMP_ITS_pipeline
PennChopMicrobiomeProgram/PhylogeneticProfiler
A short wrapper for profiling composition of microbial communities from shotgun metagenomic data.
PennChopMicrobiomeProgram/Rout_Tanes_SIV_ART_microbiome
PennChopMicrobiomeProgram/TagSequencingPipeline
PennChopMicrobiomeProgram/wfrcwf
PennChopMicrobiomeProgram/whatbacteria
Database of bacterial phenotypes and antibiotic susceptibility