waldronlab/bugSigSimple

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R
Created over 5 years ago
Updated 3 months ago

waldronlab/bugSigSimple

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Simple exploratory analysis of curated microbe signatures

Statistical-Rethinking

An interactive online reading of McElreath's Statistical Rethinking

curatedMetagenomicData

Curated Metagenomic Data of the Human Microbiome

data-science-seminar

Topics In Data Science and Bioinformatics

MultiAssayExperiment

Bioconductor package for management of multi-assay data

HGNChelper

Identify and correct invalid gene symbols

lefser

R implementation of the LEfSe method

curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

The-Art-of-Data-Science

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

cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

curatedMetagenomicDataCuration

Sample Metadata Curation for curatedMetagenomicData

TCGAutils

Toolbox package for organizing and working with TCGA data

curatedMetagenomicDataAnalyses

Analyses in R and Python Using curatedMetagenomicData

ProjectAsPackage

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

enrichOmics

Functional enrichment analysis of high-throughput omics data

MultiAssayWorkshop

Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment

SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets

CNVWorkshop

Workshop for CNV analysis with Bioconductor

AppStatBio

Applied Statistics for High-Throughput Biology

MicrobiomeWorkshop

A workshop on microbiome analysis using Bioconductor

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.

GSEABenchmarkeR

Reproducible GSEA Benchmarking

BiocNYC

Materials presented at the BiocNYC meet-up

curatedOvarianData

The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer

BugSigDBcuration

For documenting issues related to BugSigDB curation.

HMP16SData

16S rRNA Sequencing Data from the Human Microbiome Project

bioconductor

Docker container built on bioconductor/bioconductor_docker

GSEABenchmarking

Data and analysis vignette for the GSEA Benchmarking manuscript

BugSigDB

A microbial signatures database

CNVRanger

Functionality for CNV analysis

MultiAssayExperiment.TCGA

subtypeHeterogeneity

Tumor subclonality of expression-based cancer subtypes

bugphyzz

Harmonized annotation of microbial physiology

presentations

A repository for public presentations

nychanesmicrobiome

Microbiome analysis of the NYC-HANES study

doppelgangR

Identify possibly duplicate samples in a list of ExpressionSets

BIOS2

Biostatistics 621 / 821

Jupyter Notebook

MultiAssayExperiment-CCLE

curatedMetagenomicDataTerminal

A Command-Line Interface for curatedMetagenomicData

AnVILWorkshop

AnVIL/Terra workshop for Bioconductor conference

bugsigdbr

R-side access to published microbial signatures from BugSigDB

curatedMetagenomicDataPipeline

The Preprocessing Pipeline for curatedMetagenomicData

curatedTCGAWorkshop

Workshop material for the BiocNYC R/Bioconductor

MultiAssayExperimentWorkshop

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

OmicsMLRepoData

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

cheatsheets

WaldronLab Cheat Sheets

metadataClientR

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

bioc_docker

MultiAssayExperiment_Bioc2016

BugSigDBExports

BugSigDB data files

ImageSC

bugphyzzExports

oncoKBData

taxPPro

bugphyzzAnalyses

Analyses with data and signatures imported from the bugphyzz package.

waldronlab.r-universe.dev

https://waldronlab.r-universe.dev/

MetagenomicsClient

API client for curated metagenomics

MultiAssayShiny

A shiny tool for exploring MultiAssayExperiment methods

utils

Misc. scripts for assorted tasks

cacheur

MicrobiomeOntology

BugSigDBStats

BugSigDB Stats and Analysis

MultiAssayExperiment-NCI60

MultiAssayExperiment creation for NCI60 data