Waldron Lab at the CUNY SPH (@waldronlab)
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Top repositories

1

Statistical-Rethinking

An interactive online reading of McElreath's Statistical Rethinking
Rebol
125
star
2

curatedMetagenomicData

Curated Metagenomic Data of the Human Microbiome
R
125
star
3

data-science-seminar

Topics In Data Science and Bioinformatics
HTML
78
star
4

MultiAssayExperiment

Bioconductor package for management of multi-assay data
R
69
star
5

HGNChelper

Identify and correct invalid gene symbols
R
55
star
6

lefser

R implementation of the LEfSe method
R
43
star
7

curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
R
43
star
8

The-Art-of-Data-Science

An interactive online reading of Matsui and Peng's The Art of Data Science
33
star
9

cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
R
30
star
10

curatedMetagenomicDataCuration

Sample Metadata Curation for curatedMetagenomicData
R
28
star
11

TCGAutils

Toolbox package for organizing and working with TCGA data
R
23
star
12

curatedMetagenomicDataAnalyses

Analyses in R and Python Using curatedMetagenomicData
Python
22
star
13

ProjectAsPackage

Demonstration of the use of an R package to organize a data analysis project
R
21
star
14

enrichOmics

Functional enrichment analysis of high-throughput omics data
Dockerfile
20
star
15

MultiAssayWorkshop

Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment
TeX
19
star
16

SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets
R
17
star
17

CNVWorkshop

Workshop for CNV analysis with Bioconductor
R
17
star
18

AppStatBio

Applied Statistics for High-Throughput Biology
16
star
19

MicrobiomeWorkshop

A workshop on microbiome analysis using Bioconductor
R
14
star
20

PublicDataResources

Public data resources and Bioconductor: The goal of this workshop is to introduce Bioconductor packages for finding, accessing, and using large-scale public data resources including the Gene Expression Omnibus GEO, Sequence Read Archive SRA, the Genomic Data Commons GDC, and Bioconductor-hosted curated data resources for metagenomics, pharmacogenomics PharmacoDB, and The Cancer Genome Atlas.
Dockerfile
14
star
21

GSEABenchmarkeR

Reproducible GSEA Benchmarking
R
13
star
22

BiocNYC

Materials presented at the BiocNYC meet-up
HTML
12
star
23

curatedOvarianData

The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer
R
11
star
24

BugSigDBcuration

For documenting issues related to BugSigDB curation.
10
star
25

HMP16SData

16S rRNA Sequencing Data from the Human Microbiome Project
R
9
star
26

bioconductor

Docker container built on bioconductor/bioconductor_docker
Shell
8
star
27

GSEABenchmarking

Data and analysis vignette for the GSEA Benchmarking manuscript
HTML
8
star
28

BugSigDB

A microbial signatures database
JavaScript
7
star
29

CNVRanger

Functionality for CNV analysis
R
7
star
30

MultiAssayExperiment.TCGA

R
7
star
31

subtypeHeterogeneity

Tumor subclonality of expression-based cancer subtypes
R
6
star
32

bugphyzz

Harmonized annotation of microbial physiology
R
5
star
33

presentations

A repository for public presentations
TeX
5
star
34

nychanesmicrobiome

Microbiome analysis of the NYC-HANES study
HTML
4
star
35

doppelgangR

Identify possibly duplicate samples in a list of ExpressionSets
R
4
star
36

BIOS2

Biostatistics 621 / 821
Jupyter Notebook
3
star
37

MultiAssayExperiment-CCLE

R
3
star
38

curatedMetagenomicDataTerminal

A Command-Line Interface for curatedMetagenomicData
R
3
star
39

AnVILWorkshop

AnVIL/Terra workshop for Bioconductor conference
Dockerfile
3
star
40

bugsigdbr

R-side access to published microbial signatures from BugSigDB
R
3
star
41

bugSigSimple

Simple exploratory analysis of curated microbe signatures
R
3
star
42

curatedMetagenomicDataPipeline

The Preprocessing Pipeline for curatedMetagenomicData
R
2
star
43

curatedTCGAWorkshop

Workshop material for the BiocNYC R/Bioconductor
R
2
star
44

MultiAssayExperimentWorkshop

A workshop on multi-omics data representation and analysis with MultiAssayExperiment
2
star
45

OmicsMLRepoData

Translate Bioconductor resources into AI/ML-ready format + Manual curation/harmonization of the metadata for improved usability
R
2
star
46

cheatsheets

WaldronLab Cheat Sheets
1
star
47

metadataClientR

R client for http://cmgd.waldronlab.io/api-docs/
R
1
star
48

bioc_docker

Shell
1
star
49

MultiAssayExperiment_Bioc2016

R
1
star
50

BugSigDBExports

BugSigDB data files
R
1
star
51

ImageSC

R
1
star
52

bugphyzzExports

R
1
star
53

oncoKBData

R
1
star
54

taxPPro

R
1
star
55

bugphyzzAnalyses

Analyses with data and signatures imported from the bugphyzz package.
R
1
star
56

waldronlab.r-universe.dev

https://waldronlab.r-universe.dev/
1
star
57

MetagenomicsClient

API client for curated metagenomics
Python
1
star
58

MultiAssayShiny

A shiny tool for exploring MultiAssayExperiment methods
R
1
star
59

utils

Misc. scripts for assorted tasks
Shell
1
star
60

cacheur

R
1
star
61

MicrobiomeOntology

Dockerfile
1
star
62

BugSigDBStats

BugSigDB Stats and Analysis
HTML
1
star
63

MultiAssayExperiment-NCI60

MultiAssayExperiment creation for NCI60 data
R
1
star