tiagochst
Tiago Chedraoui Silva
Recently Published
BEATAML1.0-COHORT MAF
BEATAML1.0-COHORT MAF
MethReg question
MethReg question
TCGAbiolinks_issue_562
TCGAbiolinks_issue_562
TCGAbiolinks_issue_517
TCGAbiolinks_issue_517
ELMER question positive correlation
ELMER question positive correlation
TCGAbiolinks issue 523
TCGAbiolinks issue 523
MAF TCGA-CHOL legacy
MAF TCGA-CHOL legacy
Workshop for ATAC-Seq analysis
Workshop for ATAC-Seq analysis
TCGA ESCA - ATAC-seq and RNA-seq
Creating a MAE object with TCGA ATAC-seq and RNA-seq
GDC indexed vs XML
GDC indexed vs XML
DMC test
TCGAbiolinks DMC test
Meta-analysis with matched samples (by age at death and sex)
Meta-analysis with matched samples (by age at death and sex)
Correlation of AD associated methylation changes with expressions of nearby genes
Correlation of AD associated methylation changes with expressions of nearby genes
Enrichment analysis of significant CpGs after inflation correction by bacon method
Enrichment analysis of significant CpGs after inflation correction by bacon method
Meta analysis using bacon inflation- and bias-corrected P-values
Meta analysis using bacon inflation- and bias-corrected P-values
Sensitivity Analysis - estimation of genomic inflation
Sensitivity Analysis - estimation of genomic inflation
GISTIC
GISTIC
Impute missing values with impute.knn
Impute missing values with impute.knn
Read length GDC
Read length GDC
Read length
GDC Read length
ROSMAP dataset
ROSMAP dataset
Supplemental AD London
Supplemental AD London
GASPARONI dataset
GASPARONI dataset
MtSinai dataset
MtSinai dataset
Meta-analysis
Meta-analysis
London Brain blood correlation
London Brain blood correlation
Enrichment analysis
Enrichment analysis
Matched analysis
Matched analysis
Overlap with genetic susceptibility loci
Overlap with genetic susceptibility loci
Correlation of AD associated methylation changes with expressions of nearby genes
Correlation of AD associated methylation changes with expressions of nearby genes
Checking subtype information
https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/388
DREAM challenge submission
DREAM challenge submission
TCGA count
Check number of samples in TCGA
TCGA-COAD_READ
TCGA-READ-COAD stage II and III primary tumors samples with DNA methylation, gene expression and survival information.
ELMER EPIC MAE
ELMER EPIC MAE
Get normal data TCGA
Get normal data TCGA
GDC annotations for male/female, stratified by tumor type
GDC annotations for male/female, stratified by tumor type
MMRF-COMMPASS
MMRF-COMMPASS
COAD_drug_chemo
COAD drug
TCGA-SARC - HTSeq - Counts
TCGA-SARC - HTSeq - Counts
Simple nucleotide variation - hg19
Simple nucleotide variation - hg19
ESCA MAE check
ESCA MAE check
LUAD DNA methylation data
TCGA LUAD DNA methylation data - data retrieval and processing
linkedOmics
linkedOmics to be added to TCGAbiolinks
RNA-seq and protein data
RNA-seq and protein data
TCGAbiolinks - Genes not mapped ID
TCGAbiolinks - Genes not mapped ID
TCGAbiolinks to DESEq2
TCGAbiolinks to DESEq2
TCGAbiolinks - Case submitter ID
TCGAbiolinks - Case submitter ID
TCGAbiolinks - miRNA gene quantification - file.type filter
TCGAbiolinks - miRNA gene quantification - file.type filter examples
TCGAbiolinks - checking bug 367
TCGAbiolinks - checking bug 367
RNA-seq data - checking non TCGA/TARGET projects
RNA-seq data - checking non TCGA/TARGET projects
TCGAbiolinks downloading RNA-seq new projects
TCGAbiolinks downloading RNA-seq new projects
Clinical and Biospecimen BCR Biotab
Access Clinical and Biospecimen BCR Biotab with TCGAbiolinks
cRegulome
cRegulome
Clinical data - checking non TCGA/TARGET projects
Clinical data - checking non TCGA/TARGET projects
ELMER workshop reduced
ELMER workshop reduced version
TCGA data workshop
Workshop about TCGA data analysis
P-value inconsistency - correlation analysis
P-value inconsistency - correlation analysis
Comparing mouse and human genes
Comparing mouse and human genes
Workshop for multi-omics analysis with ELMER - retrieving TCGA data
Workshop for multi-omics analysis with ELMER - retrieving TCGA data
TCGA atac seq workshop
TCGA atac seq workshop
Workshop for multi-omics analysis with ELMER
Workshop for multi-omics analysis with ELMER
GDC_DNA_methylation_QC_analysis_associations_hg19_vs_hg38
GDC DNA methylation QC analysis associations. Comparing hg19 legacy annotation and hg38 annotation.
ELMER v2: supervised vs unsupervised analysis
Supplementary document to questions from reviewers
ELMER v2: supplementary document 2
supplementary document to questions from reviewers
GDC_DNA_methylation_associations_hg19_vs_hg38
Report comparing GDC DNA methylation 450K array associations from hg19 and hg38 metadata
Hg38 vs h19 annotation DNA methylation
GDC - hg38 vs h19 annotation DNA methylation
TCF7L2 targets
Evaluation enrichement of ELMER predicted TCF7L2 targets
ELMER - comparing two-tailed vs one-tailed test
This documents evaluates the DMC analysis using one-tailed test followed by FDR correction vs two-tailed test vs FDR correction
TCGAbiolinks Examples
Some examples of TCGAbiolinks that uses GDC API
ggiraph boxplot
Test