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50 results • Page
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Showing top results for tag:
tcga
•
reset
2
votes
6
replies
115
views
Meaning letters in TCGA sample barcode field
GDC
Barcode
TCGA
16 hours ago by
sumitguptabt
• 0
0
votes
0
replies
59
views
Controlled vs Public MAFs
GDC
TCGA
MAF
9 days ago by
Jn Rmro
• 0
1
vote
2
replies
252
views
TCGABioLinks getManifest() function. How to alter saved file name?
TCGA
R
Bioconductor
updated 12 days ago by
Jn Rmro
• 0 • written 12 weeks ago by
ivykosater
• 0
5
votes
3
replies
197
views
Unable to match Ensembl IDs from TCGA-related CNV datasets
Ensembl
Number
TCGA
TCGABiolinks
Variation
Copy
updated 9 days ago by
Kevin Blighe
72k • written 13 days ago by
dc37
▴ 20
2
votes
2
replies
259
views
Survival analysis
Cutoff
TCGA
updated 19 days ago by
Santosh Anand
5.3k • written 19 days ago by
wenbinm
▴ 30
224
votes
175
replies
68k
views
72 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
TCGA
Survival
Tutorial
updated 21 days ago by
Ram
32k • written 5.7 years ago by
TriS
★ 4.3k
4
votes
2
replies
382
views
Extracting specific cancer types from MAF (Mutation Annotation Format) files from TCGA(The Cancer Genome Atlas)
ENCODE
mutation
maf
TCGA
cancer
23 days ago by
peter
▴ 10
2
votes
2
replies
222
views
Question regarding TCGA and TCGAbiolinks --> RNAseq data as HTseq-Counts, FPKM, FPKM-UQ
RNAseq
FPKM-UQ
FPKM
TCGAbiolinks
TCGA
23 days ago by
miky.zo
▴ 60
0
votes
0
replies
380
views
TCGAbiolinks -> Gene ID totally missing in downloaded data.. A bug of the package or a problem with GDC data?
TCGA
GDC
TCGAbiolinks
R
26 days ago by
miky.zo
▴ 60
0
votes
2
replies
89
views
Problems specifying data.type and sample.type in TCGAbiolinks GDCquery
tcga
tcgabiolinks
r
updated 5 weeks ago by
EagleEye
6.8k • written 5 weeks ago by
loughrae
▴ 70
0
votes
0
replies
169
views
Does anyone succeded clustering TCGA data?
RNA-Seq
TCGA
clustering
updated 5 weeks ago by
Biostar
20 • written 10 weeks ago by
Omar Mohamed
• 0
0
votes
0
replies
97
views
Finding mutational burden in TCGA dataset
genome
python
UTR
tcga
cancer
5 weeks ago by
Jamie Watson
• 0
2
votes
4
replies
224
views
Understanding TCGA's ASCAT copy number data
tcga
ascat
copy number
updated 6 weeks ago by
Kevin Blighe
72k • written 6 weeks ago by
loughrae
▴ 70
5
votes
6
replies
2.4k
views
What batch correction was applied to pan-Cancer mRNA expression data?
TCGA
pan-Cancer Atlas
mRNA
normalisation
updated 6 weeks ago by
chengdu_1982
• 0 • written 2.3 years ago by
user31888
▴ 100
0
votes
0
replies
130
views
Tumor mutation burden data
sequencing
TCGA
7 weeks ago by
wenbinm
▴ 30
7
votes
18
replies
2.6k
views
problem in matching the names between file names and patients Id in TCGA
TCGA
CNV
problem in matching
updated 7 weeks ago by
HB
• 0 • written 2.9 years ago by
nazaninhoseinkhan
▴ 410
0
votes
0
replies
120
views
What is the cut off used in TCGA vcf files for allelic frequency for calling it as somatic?
tcga
vcf
8 weeks ago by
dare_devil
★ 1.4k
0
votes
0
replies
107
views
VCF files unannotated files from The Cancer Genome Atlas
tcga
vcf
9 weeks ago by
yussab
▴ 30
4
votes
11
replies
2.1k
views
Retrieve TCGA file ID and associated barcode with TCGAbiolinks: "GDC server down"
TCGA
TCGAbiolinks
GenomicDataCommons
updated 9 weeks ago by
1830416019
• 0 • written 2.7 years ago by
user31888
▴ 100
3
votes
5
replies
463
views
Getting RNA expression from TCGA only for these patients IDs
TCGA
r
RNA-Seq
updated 9 weeks ago by
1830416019
• 0 • written 17 months ago by
A
★ 3.9k
0
votes
0
replies
121
views
Calling UTRs in TCGA dataset
TCGA
cancer
UTR
ORF
10 weeks ago by
Jamie Watson
• 0
1
vote
7
replies
1.3k
views
List of TCGA genes differentially expressed in normal versus tumor
RNA-Seq
TCGA
updated 10 weeks ago by
EagleEye
6.8k • written 2.1 years ago by
jamespower
▴ 50
0
votes
2
replies
264
views
RNA seq analysis with TCGA
cbioportal
normalisation
RNA-Seq
TCGA
10 weeks ago by
najioumayma
▴ 10
2
votes
2
replies
173
views
RNAseq normal matches using publicly available databases
RNA-Seq
TCGA
DGE
normal
tumor
updated 10 weeks ago by
ATpoint
48k • written 10 weeks ago by
geneart$$
▴ 40
1
vote
4
replies
259
views
Differential gene set analysis on TCGA data
RNA-Seq
R
TCGA
updated 10 weeks ago by
Elucidata
▴ 240 • written 11 weeks ago by
hsnikdo
• 0
0
votes
0
replies
137
views
Using TCGABioLinks to query multiple cancer studies
RNA-Seq
R
TCGA
11 weeks ago by
ivykosater
• 0
2
votes
1
reply
311
views
How can I identify and remove outliers samples based on a MDS plot (limma package)?
r
edger
limma
rna-seq
tcga
updated 11 weeks ago by
seidel
7.6k • written 12 weeks ago by
andresllucena
• 0
0
votes
0
replies
122
views
Clonality Estimates of SCNA in TCGA samples
TCGA
Data repository
12 weeks ago by
christoph.kreitzer93
• 0
0
votes
3
replies
141
views
Creating a cls file from two groups of TCGA RNA-seq samples
TCGA
RNA-Seq
R
GSEA
updated 12 weeks ago by
Kevin Blighe
72k • written 12 weeks ago by
ivykosater
• 0
0
votes
3
replies
210
views
How do i create and populates new sample columns based on values (samples barcodes) from an existing column
R
TCGA
12 weeks ago by
andresllucena
• 0
1
vote
2
replies
1.1k
views
Identifying 5p and 3p in miRNA isoform expression data from TCGA for feature selection
tcga
microrna
mirna
isoform
data processing
updated 12 weeks ago by
andresllucena
• 0 • written 2.5 years ago by
jiaqiwu
▴ 10
0
votes
0
replies
145
views
Error when using TCGA CNA data to run ABSOLUTE
tcga
copynumber
absolute
12 weeks ago by
Mark
• 0
0
votes
2
replies
140
views
TCGA capture kits VCRome
tcga
captureKit
NGS
coverage
12 weeks ago by
noshadho
▴ 20
0
votes
3
replies
109
views
Compare mutation frequencies in TCGA and cbioportal
TCGA
frequency
mutation
Fisher's exact
updated 3 months ago by
Ram
32k • written 3 months ago by
P
▴ 10
12
votes
10
replies
6.8k
views
How To Use Maf Files In The Absolute Software
maf
tcga
copynumber
mutation
somatic
updated 3 months ago by
dv.sobral
• 0 • written 7.2 years ago by
Danielk
▴ 610
1
vote
3
replies
326
views
TCGAbiolinks workflow to perform differential expression analysis using limma method
RNA-Seq
TCGA
limma
TCGAbiolinks
R
3 months ago by
emibaffo
▴ 20
0
votes
0
replies
174
views
Survival analysis using copy number genes
TCGA
survival analysis
copy number variation
3 months ago by
anjuraas
▴ 10
55
votes
92
replies
8.8k
views
6 follow
How to extract the list of genes from TCGA CNV data
TCGA
CNV
genes
updated 3 months ago by
ycding
• 0 • written 3.0 years ago by
Chaimaa
▴ 250
0
votes
1
reply
246
views
TCGA miRNA analysis workflow
tcga
RNA-Seq
3 months ago by
bzzzz18
• 0
0
votes
1
reply
159
views
Paired Tumor and Normal Sample for BRCA-Subtype
TCGAbiolinks
R
TCGA
4 months ago by
kamalikaray1792
▴ 10
0
votes
0
replies
147
views
finding isomiR annotation for TCGA data using API (Python)
python
tcga
isomiR
annotation
4 months ago by
adeline
• 0
70
votes
13
replies
11k
views
12 follow
Tutorial:
Exploring cancer mutation data portals
Cancer
Data Portal
Mutation
TCGA
ICGC
Tutorial
4 months ago by
Malachi Griffith
18k
41
votes
6
replies
9.6k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf
vcf
ensembl
tcga
somatic
Tutorial
4 months ago by
Cyriac Kandoth
5.5k
0
votes
1
reply
172
views
TCGA BRCA data composition
TCGA
survival analysis
4 months ago by
wenbinm
▴ 30
0
votes
0
replies
173
views
Beta values of methylation data: mean or median? how to create an event?
R
TCGA
Methylation
illumina
4 months ago by
deathmagnetic20
▴ 10
1
vote
4
replies
292
views
Method to classify given sample into subtype
RNA-Seq
TCGA
TCGA-BRCA
Breast Cancer
Beginner
updated 4 months ago by
Biostar
20 • written 6 months ago by
im
• 0
0
votes
0
replies
173
views
Find conditions where target gene is most differentially expressed (CBioPortal/TCGA)
tcga
cbioportal
bioinformatics
4 months ago by
Dirk
▴ 80
0
votes
1
reply
232
views
How to download TCGA normal sample ?
TCGA
RNA-Seq
R
4 months ago by
najioumayma
▴ 10
6
votes
10
replies
416
views
Differential gene expression analysis of publicly available TCGA data - best practices?
rna-seq
R
deseq2
tcga
updated 4 months ago by
Kevin Blighe
72k • written 4 months ago by
MieszkoL
▴ 10
1
vote
2
replies
314
views
Survival analysis based on a set of genes for TCGA data
tcga
r
RNA-Seq
survival
updated 4 months ago by
Hamid Ghaedi
★ 1.3k • written 4 months ago by
biostarukha
▴ 10
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