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388
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How to import downloaded multiple TCGA data in R?
TCGAbiolinks R TCGA
updated 15 months ago by 82k • written 15 months ago by ▴ 110
1
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2
replies
694
views
Is it possible to estimate the concentration or amount of cellular mRNA using RNA-Seq data?
RNA-seq DEG
updated 14 months ago by ▴ 20 • written 15 months ago by ▴ 110
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0
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376
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How to show the correlation between the expression of one gene and all the cell miRNAs expression levels?
expression miRNA correlation
15 months ago by Zahra ▴ 110
6
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1
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624
views
Which one do you recommend for the problem with the smaller number of normal samples of TCGA?
DESeq2 GTEx TCGA
updated 18 months ago by 19k • written 18 months ago by ▴ 110
1
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1
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509
views
Does a TCGA dataset need batch effect removal?
effect batch TCGA
updated 18 months ago by 3.2k • written 19 months ago by ▴ 110
1
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0
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458
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microRNAs that can be downloaded from the TCGA are mature or precursor or unknown ?
DEA TCGA microRNA miRNA-Seq
20 months ago by Zahra ▴ 110
2
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2
replies
661
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What if we have low log2FC and significant adj p-value for a gene?
DEA log2FC
updated 20 months ago by ★ 27k • written 20 months ago by ▴ 110
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0
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634
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Comment: Comment: Why a gene with amplification in copy number shows downregulation in transcripto
20 months ago by Zahra ▴ 110
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2
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634
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Why a gene with amplification in copy number shows downregulation in transcriptome level?
gene alteration DEG CNV amplification
20 months ago by Zahra ▴ 110
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0
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323
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Does PCAWG have any advantage compared to TCGA for studying protein-coding regions?
TCGA PCAWG
21 months ago by Zahra ▴ 110
1
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3
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763
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Is the promoter part of whole of gene in the UCSC database?
UCSC VCF BED promoter
updated 21 months ago by 161k • written 21 months ago by ▴ 110
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0
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712
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Comment: Comment: Why a gene in UCSC has different positions?
21 months ago by Zahra ▴ 110
2
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3
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712
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Why a gene in UCSC has different positions?
UCSC BED
updated 21 months ago by ★ 2.9k • written 21 months ago by ▴ 110
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1
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504
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How to find the position of genes that their variants called by hs37d5?
hs37d5 PCAWG
updated 21 months ago by 161k • written 21 months ago by ▴ 110
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0
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943
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Comment: Comment: A question about BED file and finding mutation in vcf file
22 months ago by Zahra ▴ 110
5
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3
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943
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A question about BED file and finding mutation in vcf file
VCF BED
22 months ago by Zahra ▴ 110
1
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1
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620
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How to subset the mutations that occur just in my interest genes within the vcf file?
vcf vcftools BED
updated 22 months ago by 82k • written 22 months ago by ▴ 110
6
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2
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3.1k
views
How to add color gradient guide to my FeaturePlot?
Seurat FeaturePlot
updated 22 months ago by ★ 1.2k • written 22 months ago by ▴ 110
0
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1
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916
views
Comment: Comment: How to find DEG within a cluster between two groups without any replication info
23 months ago by Zahra ▴ 110
1
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3
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916
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How to find DEG within a cluster between two groups without any replication information in scRNA-Seq analysis?
scRNA-Seq Seurat Pseudobulk
updated 23 months ago by ▴ 700 • written 23 months ago by ▴ 110
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0
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2.5k
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Comment: Comment: How can I find DEGs between groups in one cluster of scRNA-Seq Seurat object?
23 months ago by Zahra ▴ 110
3
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3
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1.2k
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Why after normalization of scRNA-Seq data by DESeq2 the p-value of a large number of genes equal zero? How to deal with them?
scRNA-Seq DEG DESeq2 volcano Seurat
updated 23 months ago by ▴ 190 • written 23 months ago by ▴ 110
2
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2
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793
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By what criteria I can filter the somatic variants after annotation?
vcf ANNOVAR variant filter
updated 23 months ago by ▴ 910 • written 23 months ago by ▴ 110
1
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4
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2.5k
views
How can I find DEGs between groups in one cluster of scRNA-Seq Seurat object?
Seurat scRNA-Seq
23 months ago by Zahra ▴ 110
0
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1
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627
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Is it representative to use the minimal matched data of RNA-Seq in TCGA?
RNA-Seq TCGA
updated 2.2 years ago by ★ 1.2k • written 2.6 years ago by ▴ 110
1
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1
reply
567
views
Why are some tumor suppressor genes upregulate in tumors or oncogenes downregulate?
TP53 oncogenes
updated 2.3 years ago by 27k • written 2.3 years ago by ▴ 110
1
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0
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428
views
Differential expression analysis for genes in different stages of cancer by TCGA clinical data
RNA-Seq clinical DEA TCGA TNM staging
2.3 years ago by Zahra ▴ 110
0
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0
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433
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About outliers and non -separated samples in PCA
PCA DESeq2 TCGA RNA-Seq
2.4 years ago by Zahra ▴ 110
1
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1
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1.7k
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Comment: Comment: When I change samples grouping for normalization by DESeq2 I get different resul
2.5 years ago by Zahra ▴ 110
0
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0
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1.7k
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Comment: Comment: When I change samples grouping for normalization by DESeq2 I get different resul
2.5 years ago by Zahra ▴ 110
3
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5
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1.7k
views
When I change samples grouping for normalization by DESeq2 I get different results, Why?
DESeq2 TCGA volcano RNA-Seq
updated 2.5 years ago by 8.9k • written 2.5 years ago by ▴ 110
1
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2
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1.5k
views
When I convert the Ensembl IDs to gene symbols, why lots of genes are duplicated?
Ensembl raw TCGA counts RNA-Seq
updated 2.5 years ago by 14k • written 2.5 years ago by ▴ 110
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0
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1.2k
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Comment: Comment: Converting Ensembl gene id to Gene symbol
2.6 years ago by Zahra ▴ 110
3
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2
replies
1.2k
views
Converting Ensembl gene id to Gene symbol
Ensembl TCGAbiolinks biomaRT
2.6 years ago by Zahra ▴ 110
0
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0
replies
1.9k
views
Comment: Comment: converting annovar format file to maf by annovarToMaf
2.6 years ago by Zahra ▴ 110
0
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2
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1.9k
views
converting annovar format file to maf by annovarToMaf
maftools annovarToMaf ANNOVAR MAF
2.6 years ago by Zahra ▴ 110
0
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0
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565
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Should I convert the VCF file to MAF for visualizing my data?
lolliplot VCF oncoplt MAF
2.7 years ago by Zahra ▴ 110
0
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0
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1.5k
views
Comment: Comment: Can non-driver mutations disrupt the function of proteins and further affect a c
2.7 years ago by Zahra ▴ 110
7
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6
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1.5k
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Can non-driver mutations disrupt the function of proteins and further affect a cellular pathway?
driver somatic annotation VCF oncoplot
updated 2.7 years ago by ▴ 1000 • written 2.7 years ago by ▴ 110
1
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1
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755
views
How to merge multiple patient's vcf files (indel and snv) with different IDs?
vcf gatk
updated 2.7 years ago by ★ 2.9k • written 2.7 years ago by ▴ 110
2
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2
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949
views
How to give multiple input files to the gatk ?
dictionary vcf gatk
updated 2.8 years ago by ★ 1.2k • written 2.8 years ago by ▴ 110
1
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1
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584
views
How to perform differential expression analysis without the matched normal tissue data?
RNA-Seq Differential Expression DE ICGC PCAWG
updated 2.8 years ago by 82k • written 2.8 years ago by ▴ 110
0
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0
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417
views
What should I write after --operation in ANNOVAR for my interest database ?
ANNOVAR CIViC annotation DoCM VCF
2.8 years ago by Zahra ▴ 110
0
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1
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6.2k
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Comment: Comment: open-cravat: variant annotation tool
2.8 years ago by Zahra ▴ 110
0
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1
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1.4k
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Comment: Comment: Preparing CHASMplus database for annotation
2.8 years ago by Zahra ▴ 110
0
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1
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1.4k
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Comment: Comment: Preparing CHASMplus database for annotation
2.8 years ago by Zahra ▴ 110
1
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5
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1.4k
views
Preparing CHASMplus database for annotation
ANNOVAR CHASM CHASMplus annotation
updated 2.8 years ago by ▴ 1000 • written 2.9 years ago by ▴ 110
0
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1
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582
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High-throughput sequence variant analysis: Using BAM or VCF files?
ICGC VCF BAM High-throughput
updated 2.9 years ago by 82k • written 2.9 years ago by ▴ 110
0
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0
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934
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Comment: Comment: gene expression databases
2.9 years ago by Zahra ▴ 110
0
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4
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934
views
gene expression databases
GEO high-throughput GEO2R
2.9 years ago by Zahra ▴ 110
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