Bioconductor GenomicDataCommons

Showing : GenomicDataCommons • reset

votes

379

views

manifest GDCdownload GenomicDataCommons

8 months ago xiaofeiwang198266 • 0

votes

497

views

TCGA GenomicDataCommons GDC

written 10 months ago by António Miguel de Jesus Domingues ▴ 490

votes

replies

1.1k

views

TCGA GenomicDataCommons

updated 2.4 years ago by Robert Castelo ★ 3.3k • written 2.4 years ago by Hashirama ▴ 10

votes

replies

1.2k

views

GenomicDataCommons

2.7 years ago xiaofeiwang18266 ▴ 50

votes

798

views

TCGA GenomicDataCommons

3.1 years ago Ezgi ▴ 60

votes

replies

2.2k

views

GenomicDataCommons R

updated 2.7 years ago by xiaofeiwang18266 ▴ 50 • written 4.2 years ago by gv ▴ 40

votes

replies

3.8k

views

TCGAutils TCGAbiolinks GenomicDataCommons

updated 4.8 years ago by Marcel Ramos 690 • written 4.8 years ago by Dario Strbenac ★ 1.5k

votes

replies

1.1k

views

genomicdatacommons tcga gdc rest http

updated 5.3 years ago by Sean Davis 21k • written 5.3 years ago by mk ▴ 20

8 results • Page 1 of 1

Recent ...

Replies

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Comment: get BM error by Fara • 0

Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…

Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k

That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…

Votes

Answer: get BM error

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

Comment: Different Shrunk Log2FC according with reference

Reproducibility issue with scran together with lapply and BiocParallel

C: SGSeq: moving toward diffex from SGSeq analysis

Awards • All