PennChopMicrobiomeProgram

PennChopMicrobiomeProgram's repositories

ZIBR

Zero-Inflated Beta Random Effect model

Language:RNOASSERTION29 5 15

ZIR

Zero-Inflated (Wilcoxon and Kruskal–Wallis) Rank Test

Language:RMIT10 6 4

adonisplus

Language:RGPL-3.0200

mirix

Quantify the susceptibility of a bacterial community to an antibiotic.

Language:R2 30

16S_QIIME2

Snakemake based 16S QIIME2 pipeline

Language:Python100

decontam

Language:Python1 5 21

illqc

Process shotgun metagenomic DNA data for quality

Language:Python1 5 6

primertrim

Trim primers from reads

Language:Python100

reportGeneration

functions to generate basic bioinformatics overview report

Language:Python1 6 2

SampleRegistry

Web application to keep track of samples sequenced

Language:PHP1 4 5

seqBackup

Language:Python1 4 1

ShotgunPipeline

Language:Shell1 6 7

CHOP_metadata_checker

Language:HTML000

dnabc

Identify DNA barcodes in high-throughput sequencing data files

Language:PythonGPL-2.005 3

sunbeam_neutrino

Downstream analysis after using sunbeam pipeline.

Language:Python02 5

FARMM

Code used to generate the results and figures for the FARMM study.

000

gutsandcages

A package to calculate power for mouse and rat experimental design

Language:RNOASSERTION000

ITS_PIPITS_BROCC

Language:R060

microflowseq

Language:RNOASSERTION000

PathwayAbundanceFinder

A short wrapper for finding presence/absence/abundance of pathways from metagenomic data.

Language:Python06 3

PCMP_ITS_pipeline

Language:R000

PhylogeneticProfiler

A short wrapper for profiling composition of microbial communities from shotgun metagenomic data.

Language:Python05 3

Rout_Tanes_SIV_ART_microbiome

Language:R040

sbx_genome_assembly

Language:Python05 3

shotgun_alignment

Language:Python000

TagSequencingPipeline

Language:Shell05 3

wfrcwf

Language:Python000