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Comment: Comment: TPM values from TCGA datasets
15 months ago by rodolfo.peacewalker ▴ 390
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TPM values from TCGA datasets
RNAseq TPM TCGA TIMER
15 months ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: Converting transcript_count_matrix to TPM values obtained from RNA seq data
17 months ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: Converting transcript_count_matrix to TPM values obtained from RNA seq data
17 months ago by rodolfo.peacewalker ▴ 390
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BWA-MEM2 and samtools using for loop
BWA-MEM2 bash samtools
updated 23 months ago by 13k • written 23 months ago by ▴ 390
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Answer: Answer: Analyzing counts over 3 different timepoints and 2 conditions with DESeq2
2.5 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: Deseq2 Result
2.5 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: RNA-seq z-score normalization
2.5 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: What is the best way to filter out the top differentially expressed genes and de
2.5 years ago by rodolfo.peacewalker ▴ 390
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4.9k
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Answer: Answer: RNA-seq z-score normalization
2.6 years ago by rodolfo.peacewalker ▴ 390
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929
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Comment: Comment: Network analysis using distinct centrality measurements
2.6 years ago by rodolfo.peacewalker ▴ 390
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Network analysis using distinct centrality measurements
measures analysis igraph STRING centrality Network PPI
2.6 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: Filter DGElist object: keep only genes expressed in sample at the same time as a
2.6 years ago by rodolfo.peacewalker ▴ 390
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2.7k
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Comment: Comment: Filter DGElist object: keep only genes expressed in sample at the same time as a
2.6 years ago by rodolfo.peacewalker ▴ 390
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1.9k
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Comment: Comment: Filtering relevant Gene Ontology (GO) results from Gene Set Enrichment Analysis
2.6 years ago by rodolfo.peacewalker ▴ 390
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Answer: Answer: Clustering without having any replication
2.6 years ago by rodolfo.peacewalker ▴ 390
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952
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Comment: Comment: Sum of rows for GSEA analysis
2.6 years ago by rodolfo.peacewalker ▴ 390
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952
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Comment: Comment: Sum of rows for GSEA analysis
2.6 years ago by rodolfo.peacewalker ▴ 390
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1.5k
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Answer: Answer: how to build an interaction network in R
2.6 years ago by rodolfo.peacewalker ▴ 390
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4
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952
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Sum of rows for GSEA analysis
GSEA leading-edge R fGSEA
2.6 years ago by rodolfo.peacewalker ▴ 390
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2.3k
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Comment: Comment: Combining RNA-seq data from 2 experiments (DESeq2)
2.7 years ago by rodolfo.peacewalker ▴ 390
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993
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Comment: Comment: DESeq2 design question
2.7 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: RNA-seq doesn't match qPCR and western blot results
2.7 years ago by rodolfo.peacewalker ▴ 390
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1.7k
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Comment: Comment: RNA-seq doesn't match qPCR and western blot results
2.7 years ago by rodolfo.peacewalker ▴ 390
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Answer: Answer: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene
2.7 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: Pathway Analysis Interpretation
2.8 years ago by rodolfo.peacewalker ▴ 390
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608
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R is saving empty sheets for several KM plots using RTCGA package
RTCGA R
updated 13 months ago by 43k • written 2.8 years ago by ▴ 390
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936
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Comment: Comment: Pathway Analysis Interpretation
2.8 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: How install library(DESeq2), library(gplots), library(RColorBrewer) in R?
2.8 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: GSEA - Strange Results interpretation - Error in DESEQ2 ?
2.8 years ago by rodolfo.peacewalker ▴ 390
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572
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Answer: Answer: Differential expression analysis
2.8 years ago by rodolfo.peacewalker ▴ 390
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Answer: Answer: Looping over a function in R, and needing a variable name to save output as uniq
2.8 years ago by rodolfo.peacewalker ▴ 390
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4.1k
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Answer: Answer: gct output in DESeq2
2.8 years ago by rodolfo.peacewalker ▴ 390
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Answer: Answer: Proportion of RNAseq reads mapping to rRNA, tRNA, mRNA, and intergenic or antise
2.8 years ago by rodolfo.peacewalker ▴ 390
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2.2k
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Comment: Comment: Load GSEA software results into R
2.9 years ago by rodolfo.peacewalker ▴ 390
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1.5k
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Answer: Answer: How we can use DEG data for DSEA analysis
2.9 years ago by rodolfo.peacewalker ▴ 390
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3.1k
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Answer: Answer: DESeq2 count matrix read in
2.9 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: output TMM normalized counts with edgeR
2.9 years ago by rodolfo.peacewalker ▴ 390
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2.2k
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Comment: Comment: Concatenating gmt files from msigdb
2.9 years ago by rodolfo.peacewalker ▴ 390
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2.2k
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Comment: Comment: Concatenating gmt files from msigdb
2.9 years ago by rodolfo.peacewalker ▴ 390
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5
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Concatenating gmt files from msigdb
ssGSEA RNAseq Pathway KEGG REACTOME
updated 2.9 years ago by 87k • written 2.9 years ago by ▴ 390
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2.0k
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Comment: Comment: DESeq2 multiple group comparisons
3.0 years ago by rodolfo.peacewalker ▴ 390
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2.0k
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Answer: Answer: DESeq2 multiple group comparisons
3.0 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: Working with multiple bam files from tumour vs normal samps in VarScan Somatic
3.0 years ago by rodolfo.peacewalker ▴ 390
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2
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865
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Working with multiple bam files from tumour vs normal samps in VarScan Somatic
Variants DNA-seq Galaxy VCF
3.0 years ago by rodolfo.peacewalker ▴ 390
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Comment: Comment: DESeq2 adjusted p-values of 0 when p-value > 0.05
3.0 years ago by rodolfo.peacewalker ▴ 390
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4
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Looping in R to perform a GSEA analysis
RNA-Seq GSEA loops R
updated 3.0 years ago by 81k • written 3.5 years ago by ▴ 390
4
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5.5k
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Answer: Answer: How to filter out a list of specific genes from the DESeq object in R - bulk RNA
3.0 years ago by rodolfo.peacewalker ▴ 390
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938
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Answer: Answer: Differentially expression analysis
3.0 years ago by rodolfo.peacewalker ▴ 390
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1.2k
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Comment: Comment: Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
3.0 years ago by rodolfo.peacewalker ▴ 390
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