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questions
0
votes
1
reply
384
views
How to import downloaded multiple TCGA data in R?
TCGAbiolinks
R
TCGA
updated 14 months ago by
ATpoint
82k • written 14 months ago by
Zahra
▴ 110
1
vote
2
replies
691
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
Azade
▴ 20 • written 14 months ago by
Zahra
▴ 110
0
votes
0
replies
373
views
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
votes
1
reply
620
views
Which one do you recommend for the problem with the smaller number of normal samples of TCGA?
DESeq2
GTEx
TCGA
updated 17 months ago by
i.sudbery
19k • written 18 months ago by
Zahra
▴ 110
1
vote
1
reply
507
views
Does a TCGA dataset need batch effect removal?
effect
batch
TCGA
updated 18 months ago by
Hamid Ghaedi
3.2k • written 19 months ago by
Zahra
▴ 110
1
vote
0
replies
455
views
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
votes
2
replies
659
views
What if we have low log2FC and significant adj p-value for a gene?
DEA
log2FC
updated 20 months ago by
Mensur Dlakic
★ 27k • written 20 months ago by
Zahra
▴ 110
1
vote
2
replies
632
views
Why a gene with amplification in copy number shows downregulation in transcriptome level?
gene
alteration
DEG
CNV
amplification
20 months ago by
Zahra
▴ 110
0
votes
0
replies
321
views
Does PCAWG have any advantage compared to TCGA for studying protein-coding regions?
TCGA
PCAWG
21 months ago by
Zahra
▴ 110
1
vote
3
replies
758
views
Is the promoter part of whole of gene in the UCSC database?
UCSC
VCF
BED
promoter
updated 21 months ago by
Pierre Lindenbaum
161k • written 21 months ago by
Zahra
▴ 110
2
votes
3
replies
701
views
Why a gene in UCSC has different positions?
UCSC
BED
updated 21 months ago by
Papyrus
★ 2.9k • written 21 months ago by
Zahra
▴ 110
0
votes
1
reply
503
views
How to find the position of genes that their variants called by hs37d5?
hs37d5
PCAWG
updated 21 months ago by
Pierre Lindenbaum
161k • written 21 months ago by
Zahra
▴ 110
5
votes
3
replies
933
views
A question about BED file and finding mutation in vcf file
VCF
BED
21 months ago by
Zahra
▴ 110
1
vote
1
reply
619
views
How to subset the mutations that occur just in my interest genes within the vcf file?
vcf
vcftools
BED
updated 22 months ago by
ATpoint
82k • written 22 months ago by
Zahra
▴ 110
6
votes
2
replies
3.0k
views
How to add color gradient guide to my FeaturePlot?
Seurat
FeaturePlot
updated 22 months ago by
Rafael Soler
★ 1.2k • written 22 months ago by
Zahra
▴ 110
1
vote
3
replies
912
views
How to find DEG within a cluster between two groups without any replication information in scRNA-Seq analysis?
scRNA-Seq
Seurat
Pseudobulk
updated 22 months ago by
piyushjo
▴ 700 • written 22 months ago by
Zahra
▴ 110
3
votes
3
replies
1.2k
views
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
leaodel
▴ 190 • written 23 months ago by
Zahra
▴ 110
2
votes
2
replies
783
views
By what criteria I can filter the somatic variants after annotation?
vcf
ANNOVAR
variant
filter
updated 23 months ago by
Jeremy
▴ 910 • written 23 months ago by
Zahra
▴ 110
1
vote
4
replies
2.4k
views
How can I find DEGs between groups in one cluster of scRNA-Seq Seurat object?
Seurat
scRNA-Seq
22 months ago by
Zahra
▴ 110
0
votes
1
reply
627
views
Is it representative to use the minimal matched data of RNA-Seq in TCGA?
RNA-Seq
TCGA
updated 2.2 years ago by
Zhenyu Zhang
★ 1.2k • written 2.6 years ago by
Zahra
▴ 110
1
vote
1
reply
561
views
Why are some tumor suppressor genes upregulate in tumors or oncogenes downregulate?
TP53
oncogenes
updated 2.3 years ago by
Jean-Karim Heriche
27k • written 2.3 years ago by
Zahra
▴ 110
1
vote
0
replies
426
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
votes
0
replies
430
views
About outliers and non -separated samples in PCA
PCA
DESeq2
TCGA
RNA-Seq
2.4 years ago by
Zahra
▴ 110
3
votes
5
replies
1.6k
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
Friederike
8.9k • written 2.5 years ago by
Zahra
▴ 110
1
vote
2
replies
1.4k
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
swbarnes2
14k • written 2.5 years ago by
Zahra
▴ 110
3
votes
2
replies
1.1k
views
Converting Ensembl gene id to Gene symbol
Ensembl
TCGAbiolinks
biomaRT
2.5 years ago by
Zahra
▴ 110
0
votes
2
replies
1.9k
views
converting annovar format file to maf by annovarToMaf
maftools
annovarToMaf
ANNOVAR
MAF
2.6 years ago by
Zahra
▴ 110
0
votes
0
replies
563
views
Should I convert the VCF file to MAF for visualizing my data?
lolliplot
VCF
oncoplt
MAF
2.7 years ago by
Zahra
▴ 110
7
votes
6
replies
1.5k
views
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
Collin
▴ 1000 • written 2.7 years ago by
Zahra
▴ 110
1
vote
1
reply
754
views
How to merge multiple patient's vcf files (indel and snv) with different IDs?
vcf
gatk
updated 2.7 years ago by
German.M.Demidov
★ 2.9k • written 2.7 years ago by
Zahra
▴ 110
2
votes
2
replies
945
views
How to give multiple input files to the gatk ?
dictionary
vcf
gatk
updated 2.7 years ago by
vdauwera
★ 1.2k • written 2.7 years ago by
Zahra
▴ 110
1
vote
1
reply
583
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
ATpoint
82k • written 2.8 years ago by
Zahra
▴ 110
0
votes
0
replies
416
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
1
vote
5
replies
1.4k
views
Preparing CHASMplus database for annotation
ANNOVAR
CHASM
CHASMplus
annotation
updated 2.8 years ago by
Collin
▴ 1000 • written 2.9 years ago by
Zahra
▴ 110
0
votes
1
reply
579
views
High-throughput sequence variant analysis: Using BAM or VCF files?
ICGC
VCF
BAM
High-throughput
updated 2.9 years ago by
ATpoint
82k • written 2.9 years ago by
Zahra
▴ 110
0
votes
4
replies
928
views
gene expression databases
GEO
high-throughput
GEO2R
2.9 years ago by
Zahra
▴ 110
12
votes
9
replies
4.4k
views
Good annotation databases for a VCF file (somatic variants)
VCF
ANNOVAR
somatic
databases
annotation
updated 2.9 years ago by
emmanouil.a
▴ 120 • written 3.0 years ago by
Zahra
▴ 110
0
votes
0
replies
675
views
Convert different types of databases to ANNOVAR custom databases
ANNOVAR
CIViC
DoCM
annotation
VCF
2.9 years ago by
Zahra
▴ 110
2
votes
3
replies
2.0k
views
merging two VCF files
gatk
dictionary
vcf
updated 2.9 years ago by
sbstevenlee
▴ 480 • written 3.0 years ago by
Zahra
▴ 110
2
votes
1
reply
678
views
Study variation of some genes by VCF file
VCF
mutation
updated 2.9 years ago by
Ram
43k • written 2.9 years ago by
Zahra
▴ 110
5
votes
4
replies
1.1k
views
Could I analyze just a few genes of a BAM file?
RNA-Seq
BAM
updated 2.9 years ago by
Ram
43k • written 3.1 years ago by
Zahra
▴ 110
2
votes
3
replies
1.3k
views
BAM file download for just a few genes
RefSeq
BAM
position
RNA-Seq
UCSC
updated 3.1 years ago by
Jorge Amigo
14k • written 3.1 years ago by
Zahra
▴ 110
0
votes
1
reply
508
views
ICGC data download
ICGC
local server
3.2 years ago by
Zahra
▴ 110
0
votes
1
reply
618
views
cloud repository of the ICGC
ICGC
collaboratory
AWS
updated 3.2 years ago by
GenoMax
142k • written 3.2 years ago by
Zahra
▴ 110
0
votes
1
reply
1.0k
views
ICGC Raw counts for RNA-Seq data
ICGC
RNA-Seq
Raw counts
3.3 years ago by
Zahra
▴ 110
1
vote
1
reply
669
views
How correlate between transcriptome data and expression, without proteome data?
ICGC
proteome
integrated analysis
transcriptome
updated 3.3 years ago by
Carlo Yague
8.7k • written 3.3 years ago by
Zahra
▴ 110
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