Benchmarking HanniganGD_2018 data

cMD metadata overview

Pilot: Implementing PathML's stain normalization step in AnVIL/Terra

Apply RAVmodel_Human_C2 on mice T-cell data

Metadata analysis for microbiomeABX R21

Test SIAMCAT modeling on Raymond and Vincent datasets

Run bioBakery wmx workflow in Terra using RunTerraWorkflow and biobakeR pacakges

Compare random RAVs and PCSSs

Manual curation of two RAVs

Examples of not-corrected inputs for HGNChelper

Repeat CRC paper's Figure 4C with all 18 datasets

Repeat CRC paper's Figure 4C with 10 validation datasets

bioBakeryR vignettes ver2

Organize bioBakeryR outputs in SummarizedExperiment

PCAmodel comparison: Default model

PCAmodel comparison: more studies

PCAmodel comparison: top 10 PCs

PCAmodel comparison: a fewer clusters

raw counts from 483 TCGA-COAD tumor samples --> log2(TPM+1) --> subset to 13,934 genes --> rowNorm --> PCA --> geneList from PC2 --> GSEA

raw counts from 483 TCGA-COAD tumor samples --> log2(TPM+1) --> subset to 13,934 genes --> PCA --> geneList from PC2 --> GSEA

raw counts from 483 TCGA-COAD tumor samples --> log2(TPM+1) --> subset to 13,934 genes --> rowSums --> GSEA

raw counts from 483 TCGA-COAD tumor samples --> log2(TPM+1) --> rowNorm --> PCA --> build a gene list from PC2 --> GSEA

raw counts from 483 TCGA-COAD tumor samples --> log2(TPM+1) --> PCA --> build a gene list from PC3 --> GSEA

raw counts from 483 TCGA-COAD tumor samples --> log2(TPM+1) --> PCA --> build a gene list from PC1 --> GSEA

raw counts from 483 TCGA-COAD tumor samples --> log2(TPM+1) --> PCA --> build a gene list from PC2 --> GSEA

raw counts from 483 TCGA-COAD tumor samples --> log2(TPM+1) --> build a gene list based on rowSums --> GSEA

Human B-cell expression dataset validated with PCAmodel is plotted in the interactive graph.

PCAmodel from refine.bio data without controls. Subset to common genes with MSigDB C7

B-cell dataset validation using PCAmodel from hierarchical clustering

Visualization GSEA results of Cl4935_263

Negative control data + the subset of TCGA-COAD

GSEA on PCcluster 263 (Cl4935_263) to test breast-related signature

Test graph-based clustering using Girvan-Newman algorithm

Finding minimum k that separate negative controls

Compare ClusterR (different seeding) and Kmeans (different algorithm).

Use top 5 PCs from 676 refine.bio + 20 controls (pos & neg)

Search heart-disease related TOPMed cohorts

Three different PCAmodels from recount2 datasets based on their annotation database.

EDA on outliers

loading_perData (using PCA+clustering) and multiPLIER Z matrix from the same gene set

Build avgLoadings from two different processing approaches.

Analysis CNVWorkflow output - TMB, Mutational Signature, Variant Classification Accuracy

Run PureCN for CNV analysis

Prepare/ pre-processing input files for PureCN

2018 NYC R/Bioconductor Meetup

2018 NYC R/Bioconductor Meetup