Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Profile
Posts
Awards
Show
all
questions
tools
blogs
news
tutorials
forum
answers
comments
0
votes
1
reply
354
views
How to import downloaded multiple TCGA data in R?
TCGAbiolinks
R
TCGA
updated 13 months ago by
ATpoint
81k • written 13 months ago by
Zahra
▴ 110
1
vote
2
replies
655
views
Is it possible to estimate the concentration or amount of cellular mRNA using RNA-Seq data?
RNA-seq
DEG
updated 12 months ago by
Azade
▴ 20 • written 13 months ago by
Zahra
▴ 110
0
votes
0
replies
356
views
How to show the correlation between the expression of one gene and all the cell miRNAs expression levels?
expression
miRNA
correlation
14 months ago by
Zahra
▴ 110
6
votes
1
reply
595
views
Which one do you recommend for the problem with the smaller number of normal samples of TCGA?
DESeq2
GTEx
TCGA
updated 16 months ago by
i.sudbery
18k • written 16 months ago by
Zahra
▴ 110
1
vote
1
reply
473
views
Does a TCGA dataset need batch effect removal?
effect
batch
TCGA
updated 16 months ago by
Hamid Ghaedi
3.2k • written 17 months ago by
Zahra
▴ 110
1
vote
0
replies
439
views
microRNAs that can be downloaded from the TCGA are mature or precursor or unknown ?
DEA
TCGA
microRNA
miRNA-Seq
19 months ago by
Zahra
▴ 110
2
votes
2
replies
616
views
What if we have low log2FC and significant adj p-value for a gene?
DEA
log2FC
updated 19 months ago by
Mensur Dlakic
★ 26k • written 19 months ago by
Zahra
▴ 110
0
votes
0
replies
598
views
Comment:
Comment: Why a gene with amplification in copy number shows downregulation in transcripto
19 months ago by
Zahra
▴ 110
1
vote
2
replies
598
views
Why a gene with amplification in copy number shows downregulation in transcriptome level?
gene
alteration
DEG
CNV
amplification
19 months ago by
Zahra
▴ 110
0
votes
0
replies
304
views
Does PCAWG have any advantage compared to TCGA for studying protein-coding regions?
TCGA
PCAWG
19 months ago by
Zahra
▴ 110
1
vote
3
replies
728
views
Is the promoter part of whole of gene in the UCSC database?
UCSC
VCF
BED
promoter
updated 19 months ago by
Pierre Lindenbaum
160k • written 19 months ago by
Zahra
▴ 110
0
votes
0
replies
661
views
Comment:
Comment: Why a gene in UCSC has different positions?
19 months ago by
Zahra
▴ 110
2
votes
3
replies
661
views
Why a gene in UCSC has different positions?
UCSC
BED
updated 19 months ago by
Papyrus
★ 2.9k • written 19 months ago by
Zahra
▴ 110
0
votes
1
reply
478
views
How to find the position of genes that their variants called by hs37d5?
hs37d5
PCAWG
updated 20 months ago by
Pierre Lindenbaum
160k • written 20 months ago by
Zahra
▴ 110
0
votes
0
replies
887
views
Comment:
Comment: A question about BED file and finding mutation in vcf file
20 months ago by
Zahra
▴ 110
5
votes
3
replies
887
views
A question about BED file and finding mutation in vcf file
VCF
BED
20 months ago by
Zahra
▴ 110
1
vote
1
reply
600
views
How to subset the mutations that occur just in my interest genes within the vcf file?
vcf
vcftools
BED
updated 20 months ago by
ATpoint
81k • written 20 months ago by
Zahra
▴ 110
6
votes
2
replies
2.9k
views
How to add color gradient guide to my FeaturePlot?
Seurat
FeaturePlot
updated 21 months ago by
Rafael Soler
★ 1.2k • written 21 months ago by
Zahra
▴ 110
0
votes
1
reply
853
views
Comment:
Comment: How to find DEG within a cluster between two groups without any replication info
21 months ago by
Zahra
▴ 110
1
vote
3
replies
853
views
How to find DEG within a cluster between two groups without any replication information in scRNA-Seq analysis?
scRNA-Seq
Seurat
Pseudobulk
updated 21 months ago by
piyushjo
▴ 700 • written 21 months ago by
Zahra
▴ 110
0
votes
0
replies
2.2k
views
Comment:
Comment: How can I find DEGs between groups in one cluster of scRNA-Seq Seurat object?
21 months ago by
Zahra
▴ 110
3
votes
3
replies
1.1k
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 21 months ago by
leaodel
▴ 190 • written 21 months ago by
Zahra
▴ 110
2
votes
2
replies
734
views
By what criteria I can filter the somatic variants after annotation?
vcf
ANNOVAR
variant
filter
updated 21 months ago by
Jeremy
▴ 880 • written 21 months ago by
Zahra
▴ 110
1
vote
4
replies
2.2k
views
How can I find DEGs between groups in one cluster of scRNA-Seq Seurat object?
Seurat
scRNA-Seq
21 months ago by
Zahra
▴ 110
0
votes
1
reply
588
views
Is it representative to use the minimal matched data of RNA-Seq in TCGA?
RNA-Seq
TCGA
updated 2.1 years ago by
Zhenyu Zhang
★ 1.1k • written 2.4 years ago by
Zahra
▴ 110
1
vote
1
reply
536
views
Why are some tumor suppressor genes upregulate in tumors or oncogenes downregulate?
TP53
oncogenes
updated 2.1 years ago by
Jean-Karim Heriche
27k • written 2.1 years ago by
Zahra
▴ 110
1
vote
0
replies
406
views
Differential expression analysis for genes in different stages of cancer by TCGA clinical data
RNA-Seq
clinical
DEA
TCGA
TNM
staging
2.2 years ago by
Zahra
▴ 110
0
votes
0
replies
413
views
About outliers and non -separated samples in PCA
PCA
DESeq2
TCGA
RNA-Seq
2.3 years ago by
Zahra
▴ 110
1
vote
1
reply
1.6k
views
Comment:
Comment: When I change samples grouping for normalization by DESeq2 I get different resul
2.4 years ago by
Zahra
▴ 110
0
votes
0
replies
1.6k
views
Comment:
Comment: When I change samples grouping for normalization by DESeq2 I get different resul
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 2.4 years ago by
Friederike
8.9k • written 2.4 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 2.4 years ago by
swbarnes2
14k • written 2.4 years ago by
Zahra
▴ 110
0
votes
0
replies
1.1k
views
Comment:
Comment: Converting Ensembl gene id to Gene symbol
2.4 years ago by
Zahra
▴ 110
3
votes
2
replies
1.1k
views
Converting Ensembl gene id to Gene symbol
Ensembl
TCGAbiolinks
biomaRT
2.4 years ago by
Zahra
▴ 110
0
votes
0
replies
1.8k
views
Comment:
Comment: converting annovar format file to maf by annovarToMaf
2.5 years ago by
Zahra
▴ 110
0
votes
2
replies
1.8k
views
converting annovar format file to maf by annovarToMaf
maftools
annovarToMaf
ANNOVAR
MAF
2.5 years ago by
Zahra
▴ 110
0
votes
0
replies
533
views
Should I convert the VCF file to MAF for visualizing my data?
lolliplot
VCF
oncoplt
MAF
2.5 years ago by
Zahra
▴ 110
0
votes
0
replies
1.4k
views
Comment:
Comment: Can non-driver mutations disrupt the function of proteins and further affect a c
2.6 years ago by
Zahra
▴ 110
7
votes
6
replies
1.4k
views
Can non-driver mutations disrupt the function of proteins and further affect a cellular pathway?
driver
somatic
annotation
VCF
oncoplot
updated 2.6 years ago by
Collin
▴ 1000 • written 2.6 years ago by
Zahra
▴ 110
1
vote
1
reply
727
views
How to merge multiple patient's vcf files (indel and snv) with different IDs?
vcf
gatk
updated 2.6 years ago by
German.M.Demidov
★ 2.9k • written 2.6 years ago by
Zahra
▴ 110
2
votes
2
replies
892
views
How to give multiple input files to the gatk ?
dictionary
vcf
gatk
updated 2.6 years ago by
vdauwera
★ 1.2k • written 2.6 years ago by
Zahra
▴ 110
1
vote
1
reply
560
views
How to perform differential expression analysis without the matched normal tissue data?
RNA-Seq
Differential
Expression
DE
ICGC
PCAWG
updated 2.7 years ago by
ATpoint
81k • written 2.7 years ago by
Zahra
▴ 110
0
votes
0
replies
402
views
What should I write after --operation in ANNOVAR for my interest database ?
ANNOVAR
CIViC
annotation
DoCM
VCF
2.7 years ago by
Zahra
▴ 110
0
votes
1
reply
6.0k
views
Comment:
Comment: open-cravat: variant annotation tool
2.7 years ago by
Zahra
▴ 110
0
votes
1
reply
1.3k
views
Comment:
Comment: Preparing CHASMplus database for annotation
2.7 years ago by
Zahra
▴ 110
0
votes
1
reply
1.3k
views
Comment:
Comment: Preparing CHASMplus database for annotation
2.7 years ago by
Zahra
▴ 110
1
vote
5
replies
1.3k
views
Preparing CHASMplus database for annotation
ANNOVAR
CHASM
CHASMplus
annotation
updated 2.7 years ago by
Collin
▴ 1000 • written 2.8 years ago by
Zahra
▴ 110
0
votes
1
reply
558
views
High-throughput sequence variant analysis: Using BAM or VCF files?
ICGC
VCF
BAM
High-throughput
updated 2.7 years ago by
ATpoint
81k • written 2.7 years ago by
Zahra
▴ 110
0
votes
0
replies
885
views
Comment:
Comment: gene expression databases
2.8 years ago by
Zahra
▴ 110
0
votes
4
replies
885
views
gene expression databases
GEO
high-throughput
GEO2R
2.8 years ago by
Zahra
▴ 110
63 results • Page
1 of 2
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6