Bioconductor DNAStringSetList

Showing : DNAStringSetList • reset

2

votes

1

reply

952

views

dnastringset dnastringsetlist seqnames

6.1 years ago s.ghignone ▴ 10

0

votes

0

replies

870

views

biostrings DNAStringSetList

8.7 years ago Michael Love 43k

1

vote

5

replies

4.7k

views

readVcf DNAStringSet DNAStringSetList variantannotation readvcf

9.7 years ago dan.gatti • 0

3

votes

5

replies

3.4k

views

variantannotation granges DNAStringSetList findoverlaps Vranges

9.8 years ago summerela • 0

4 results • Page 1 of 1

Recent ...

Replies

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0

Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …

Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k

Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…

Comment: Build error on kunpeng2 Linux aarch64 by martin.grigorov ▴ 10

Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…

Answer: Standardization of rlog transformed counts before PCA by ATpoint ★ 4.6k

I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Also, re DMR.plot(), yes the understanding is that all DMRs from EPICv2 should be plotted in hg38. I've left that implied for the user sinc…

Votes

Comment: Feature Counts - potential bug with outfile.jcounts

Answer: Feature Counts - potential bug with outfile.jcounts

Comment: Can we get beta values with DMRcate package

Answer: Can we get beta values with DMRcate package

DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)

Awards • All

Popular Question to martin.grigorov ▴ 10

Scholar to James W. MacDonald 67k