Showing : Vranges • reset
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Formal class VRanges versus Large VRanges
somaticsignatures vranges readvcfasvranges
6.3 years ago guillaume.dachy • 0
3
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4
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2.0k
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Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 6.5 years ago by ★ 11k • written 6.5 years ago by • 0
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Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 6.5 years ago by ★ 6.8k • written 6.5 years ago by • 0
1
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2
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1.9k
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Trouble while concatenating VRanges object ()
somaticsignatures somaticsignatures package readvcfasvranges vranges
7.4 years ago • updated 7.3 years ago guillaume.dachy • 0
0
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3
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1.5k
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about VRanges and filtering somatic variants
vranges vcf to vranges
8.0 years ago Bogdan ▴ 670
1
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4
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2.1k
views
Converting VCF to VRanges
somaticsignatures vranges
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 10
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2
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1.7k
views
Combining GRange/VRange objects
granges vranges readvcfasvranges somaticsignatures
updated 8.7 years ago by ★ 11k • written 8.7 years ago by • 0
3
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9
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2.4k
views
SomaticSignatures mutationContext (char ',') not in lookup table
SomaticSignatures mutationContext VRanges
updated 9.3 years ago by ★ 1.3k • written 9.3 years ago by ▴ 10
2
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3
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2.6k
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Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation vranges readvcf readvcfasvranges metadata
9.8 years ago summerela • 0
3
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5
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Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation granges DNAStringSetList findoverlaps Vranges
9.8 years ago summerela • 0
10 results • Page 1 of 1
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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)
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