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GenomicDataCommons
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203
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Why 3 RNA-seq bams for same sample/aliquot_barcode?
manifest
GDCdownload
GenomicDataCommons
3 months ago
xiaofeiwang198266
• 0
0
votes
1
reply
338
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 5 months ago by
António Miguel de Jesus Domingues
▴ 490
3
votes
2
replies
893
views
How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA
GenomicDataCommons
updated 24 months ago by
Robert Castelo
★ 3.0k • written 24 months ago by
Hashirama
▴ 10
4
votes
4
replies
1.1k
views
2 questions: why there is nothing for file_ids? How could I generate a manifest file with filtering of Race and Ethnicity?
GenomicDataCommons
2.3 years ago
xiaofeiwang18266
▴ 50
0
votes
1
reply
669
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA
GenomicDataCommons
2.7 years ago
Ezgi
▴ 60
0
votes
4
replies
1.9k
views
extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons
R
updated 2.3 years ago by
xiaofeiwang18266
▴ 50 • written 3.8 years ago by
gv
▴ 40
5
votes
11
replies
3.4k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 4.4 years ago by
Marcel Ramos
680 • written 4.4 years ago by
Dario Strbenac
★ 1.5k
4
votes
2
replies
996
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons
tcga
gdc
rest
http
updated 4.9 years ago by
Sean Davis
21k • written 4.9 years ago by
mk
▴ 20
8 results • Page
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Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and
by
Aastha Kapoor
• 0
After several attempts the code has worked. I connected to a faster internet connection. set the timeout (1000000) and run the command. I …
Comment: DESeq2 estimateSizeFactors iterate takes too long
by
Karthik
• 0
Hello, I agree with you, and we are in process of working with collaborators, but I wanted to get a general opinion on the data and get a …
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
Guido Hooiveld
★ 3.8k
Code to show it works: > library(clusterProfiler) > > ## use provided 10 IDs, plus as last one add ID that has a GO annotati…
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
Guido Hooiveld
★ 3.8k
You are almost there... Yet - pay attention to the error message (`--> No gene can be mapped.... --> Expected input gene ID: GO:0055080, .…
Comment: Problem loading HDF5Array in R 4.3.2
by
Sarah
• 0
Thanks for the reply! I tried this and it is crashing at `h5createFile("test.h5")` even after reinstalling **Rhdf5lib** and **rhdf5** It …
Votes
Answer: Limma/DESeq2 for unbalanced nested design (paired samples)
Result from GSEA for non-model organism not as expected
Comment: DESeq2 estimateSizeFactors iterate takes too long
Answer: DESeq2 estimateSizeFactors iterate takes too long
Comment: biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl
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bas_work
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