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Showing top results for tag: tcga • reset
1
vote
1
reply
27
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Would this laptop be sufficient for small dataset/sequence analysis?
DeSEQ2 tcga Xena laptop
updated 9 minutes ago by ★ 12k • written 1 hour ago by • 0
0
votes
1
reply
78
views
Validate TCGA DEGs with GEOdatabase
DEGs TCGA GEOdatabase
updated 2 days ago by ★ 1.6k • written 3 days ago by • 0
0
votes
1
reply
102
views
Expression analysis of data obtained from Broad GDAC Firehouse (https://gdac.broadinstitute.org/)
gdac tcga
updated 4 days ago by 34k • written 22 days ago by • 0
0
votes
3
replies
1.1k
views
conversion of case_ids to file_ids TCGA data
TCGA case_ids conversion
updated 6 days ago by • 0 • written 2.2 years ago by ▴ 410
0
votes
2
replies
153
views
From case uuid to specific file uuid
TCGA GDC
5 days ago by adebola.1 • 0
0
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0
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64
views
RNA-seq raw counts normalization for survival analysis
survival tcga RNA-Seq r
8 days ago by fifty_fifty ▴ 10
0
votes
0
replies
61
views
How to perform Z-score normalization for Cox-regression analysis, based on signature enrichment within TCGA data?
cox-regression ssGSEA TCGA Z-score normalization
8 days ago by joker33 ▴ 60
0
votes
2
replies
158
views
Matching the file names with exposure file in TCGA
names FPKM file TCGA matching exposure
10 days ago by nazaninhoseinkhan ▴ 410
3
votes
2
replies
179
views
TPM to log2(TPM+1)
log TCGA KIRC RNA-seq TPM
17 days ago by David ▴ 20
2
votes
5
replies
268
views
Integration of two TCGA datasets
r RNA-Seq tcga survival
updated 22 days ago by 75k • written 22 days ago by ▴ 10
1
vote
2
replies
163
views
downloading manifest files on TCGA GDC
TCGA
22 days ago by peter ▴ 10
0
votes
0
replies
64
views
How to get transcript level estimates in TPM from TCGA BRCA
RNA-Seq BRCA TCGA
25 days ago by StartR ▴ 20
0
votes
2
replies
155
views
TCGA-BRCA download
Data Download BRCA TCGA
updated 4 weeks ago by ★ 2.1k • written 4 weeks ago by • 0
0
votes
3
replies
173
views
how can i find expressions of miRNAs using TCGA
mirna tcga
updated 28 days ago by ▴ 860 • written 4 weeks ago by ▴ 10
0
votes
1
reply
122
views
TCGA germline and somatic snvs
TCGA SNVs gdc
updated 22 days ago by ▴ 420 • written 5 weeks ago by • 0
0
votes
4
replies
192
views
TCGA Sample barcode
Tumor Barcode Normal TCGA
updated 5 weeks ago by 5.6k • written 5 weeks ago by ▴ 50
0
votes
0
replies
162
views
How to find coefficients of all genes for prediction of risk score with some threshold using multivariate cox regression model in TCGA-LIHC dataset ?
cox risk-score survival-analysis TCGA
6 weeks ago by donnieDarko • 0
0
votes
1
reply
107
views
GDC Client 500 Server Error
TCGA GDC error GDC-client server
updated 6 weeks ago by 75k • written 6 weeks ago by • 0
1
vote
4
replies
297
views
unmapped reads BAM TCGA
unmapped BAM read TCGA
updated 7 weeks ago by 104k • written 7 weeks ago by • 0
0
votes
5
replies
269
views
TCGA data Query (GDCquery): external_gene_name " are missing
DATASET GDCquery GDCprepare TCGA GDCdownload
7 weeks ago by H. Z. Amini • 0
1
vote
4
replies
226
views
gene expression for a specific gene across for multiple cancer types in TCGA datasets
gene_expression TCGA RTCAG
7 weeks ago by pt.taklifi ▴ 60
4
votes
5
replies
303
views
How to analyse TCGA CNV data with GAIA R package
CNV TCGA GAIA R
updated 7 weeks ago by 75k • written 7 weeks ago by • 0
2
votes
3
replies
243
views
Coverage data for TCGA BAM files
exome number tcga copy dna whole coverage
8 weeks ago by enho ▴ 20
1
vote
0
replies
117
views
Correlation analyses on TCGA data
TCGA edgeR Normalization TPM Correlation
8 weeks ago by mario.keller.1988 ▴ 10
1
vote
3
replies
215
views
Are raw RNA-seq data available for samples of TCGA-LUAD (TCGA data set) ?
TCGA RNAseq
updated 8 weeks ago by 104k • written 8 weeks ago by ▴ 70
0
votes
0
replies
84
views
A problem with TCGA data related to HCC
TCGA HCC HCV
8 weeks ago by Dude • 0
2
votes
2
replies
177
views
TCGA samples
TCGA Samplestype
8 weeks ago by mrashad ▴ 60
1
vote
2
replies
252
views
Download raw RNA-seq data from TCGA
TCGA RNA-seq
9 weeks ago by qwzhang0601 ▴ 70
4
votes
3
replies
220
views
Where is the most up-to date TCGA clinic data?
TCGA
updated 7 weeks ago by ▴ 420 • written 9 weeks ago by ▴ 50
0
votes
0
replies
83
views
Where to find TCGA hg38 WXS coverage per sample
TCGA WXS coverage
9 weeks ago by rebeliscu • 0
2
votes
5
replies
275
views
TCGA library type information
tcga
updated 7 weeks ago by ▴ 420 • written 9 weeks ago by ★ 3.8k
6
votes
10
replies
800
views
TCGA CNV data 1p/19q codeletion (whole arm deletion)
TCGA CNV codeletion GBM LGG
updated 9 weeks ago by ▴ 20 • written 13 months ago by ▴ 20
0
votes
7
replies
636
views
Why were all TCGA SVS slides redacted?
slides slide tcga svs digital offtopic
updated 8 weeks ago by 75k • written 3 months ago by ▴ 30
3
votes
5
replies
410
views
Single cell analysis
TCGA R singlecellanalysis scRNAseq
10 weeks ago by leticia ▴ 20
0
votes
0
replies
211
views
Information regarding OS, DFI, DSS and PFI and their time points in TCGA BRCA
R TCGA KMPlot BRCA
10 weeks ago by StartR ▴ 20
1
vote
3
replies
242
views
quering publicaly available data sets of RNA-seq and constructing a Kaplan Meier plot
Meier plot Kaplan TCGA cBioportal clinical GDC
updated 11 weeks ago by 7.0k • written 11 weeks ago by • 0
0
votes
0
replies
103
views
Local database connection and remote download error using curatedTCGAData
TCGA bioconductor r ExperimentHub
10 weeks ago by robjohn70000 ▴ 130
0
votes
2
replies
277
views
Batch effects and differential expression analysis on TCGA data for cancer subtypes
RNA-Seq TCGA batch
11 weeks ago by antmantras • 0
0
votes
0
replies
139
views
differential gene expression (DGE) using TCGABiolinks
DGE TCGA tcgabiolinks
3 months ago by peter ▴ 10
4
votes
6
replies
745
views
Understanding TCGA's ASCAT copy number data
tcga ascat copy number
updated 16 days ago by 75k • written 4 months ago by ▴ 70
6
votes
11
replies
858
views
Meaning letters in TCGA sample barcode field
GDC Barcode TCGA
updated 3 months ago by 34k • written 3 months ago by ▴ 30
0
votes
0
replies
166
views
Controlled vs Public MAFs
GDC TCGA MAF
3 months ago by Jn Rmro • 0
1
vote
2
replies
407
views
TCGABioLinks getManifest() function. How to alter saved file name?
TCGA R Bioconductor
updated 3 months ago by • 0 • written 6 months ago by • 0
5
votes
3
replies
406
views
Unable to match Ensembl IDs from TCGA-related CNV datasets
Ensembl Number TCGA TCGABiolinks Variation Copy
updated 3 months ago by 75k • written 3 months ago by ▴ 20
2
votes
2
replies
399
views
Survival analysis
Cutoff TCGA
updated 3 months ago by 5.4k • written 3 months ago by ▴ 30
229
votes
175
replies
70k
views
72 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 4 months ago by 34k • written 6.0 years ago by ★ 4.4k
4
votes
2
replies
532
views
Extracting specific cancer types from MAF (Mutation Annotation Format) files from TCGA(The Cancer Genome Atlas)
ENCODE mutation maf TCGA cancer
4 months ago by peter ▴ 10
2
votes
2
replies
334
views
Question regarding TCGA and TCGAbiolinks --> RNAseq data as HTseq-Counts, FPKM, FPKM-UQ
RNAseq FPKM-UQ FPKM TCGAbiolinks TCGA
4 months ago by miky.zo ▴ 60
0
votes
0
replies
460
views
TCGAbiolinks -> Gene ID totally missing in downloaded data.. A bug of the package or a problem with GDC data?
TCGA GDC TCGAbiolinks R
4 months ago by miky.zo ▴ 60
0
votes
2
replies
214
views
Problems specifying data.type and sample.type in TCGAbiolinks GDCquery
tcga tcgabiolinks r
updated 4 months ago by 7.0k • written 4 months ago by ▴ 70
50 results • Page 1 of 1
Recent Votes
Answer: Would this laptop be sufficient for small dataset/sequence analysis?
Answer: What's the biggest thing you dislike about bioinformatics?
Comment: opening downloaded files from STRING protein network without R
Comment: What's the biggest thing you dislike about bioinformatics?
Gene Set Enrichment Analysis
Comment: Removing genes of Seurat object during integration pipeline
How to generate a .sam/.bam file of a particular chromosome or even a particular region?
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Recent Replies
Answer: Would this laptop be sufficient for small dataset/sequence analysis? by Mensur Dlakic ★ 12k
16 GB of RAM will not cut it for any serious bioinformatics application these days. Doubly so if you choose to run Windows.
Comment: inquiry related to snpsift by Kevin Blighe 75k
I see - thanks. I am not sure that `SnpSift annotate` can do this, but you can first remove the original ID via `bcftools`, as follows: …
Answer: Forum: Job opportunities in Europe, with and without a PhD by Kevin Blighe 75k
South Africa? - very nice. I had been considering moving there, would you believe. There is no correct answer to your question, and one ca…
Comment: inquiry related to snpsift by rheab1230 • 0
the command: java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf I am getting no error. the input file …
Comment: Displaying points which fall outside of the plot window in EnhancedVolcano by os306 ▴ 10
Hi there, just to follow up on this, I used your package to generate my volcano plots and got exactly what I was looking for. I now wish to…
Comment: inquiry related to snpsift by Kevin Blighe 75k
Hi, please show: 1. the command(s) that you are using 2. a sample of your input data 3. a sample of your output data 4. any status, wa…
Comment: opening downloaded files from STRING protein network without R by fionajcunningham • 0
thanks GenoMax I will try this sorry for delay in reply!! Fiona
Comment: What's the biggest thing you dislike about bioinformatics? by WouterDeCoster 45k
The alternative, constant off-by-one errors, aren't my idea of fun either :-)
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
Yeah, you can filter min_cells in Seurat with SCtransform. That would probably change the gene numbers in the SCT assay of the object. I u…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
Doesn't sctransform has a `min_cells` parameter that you could use here? It will only consider genes detected in at least `min_cells` cells…
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
I was thinking of making it an arbitrary cut off of 10 cells, Seurat's documentation uses 3 for reading in a single sample. I believe that …
Answer: How To Split A Bam File By Chromosome by etiennedanis • 0
With samtools v1.11, ```samtools view -b in.bam chr1 > out.bam``` did not work for me. But ```samtools view -b in.bam 1 > out.bam``` wo…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
What is a "few" cells? So how many? You would need to manually calculate the fraction of cells expressing a certain gene. Not sure in which…
Comment: I want to make a graph for conserved regions by sa.youssef • 0
Thanks so much, it is a great suggestion. may I ask you if you know a way to visualize the results of these data in my report? as we are wo…
Comment: Minfi - estimateCellCounts by Papyrus ★ 1.1k
I understand that you have whole blood samples and that's why you expect them to have more granulocytes? You could also try the [ENmix][1] …
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