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getpromoterseq
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getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq
GRanges
GenomicFeatures
5.7 years ago
jerrywu1987
• 0
1
vote
5
replies
1.9k
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Extract genomic features from a TxDb-like object
TxDB
genomicfeatures
promoter
getpromoterseq
updated 6.1 years ago by
Hervé Pagès
16k • written 6.1 years ago by
rbenel
▴ 40
2
votes
6
replies
2.5k
views
Working with Arabidopsis Databases
bsgenome
biomart
getPromoterSeq
txdb
8.7 years ago
oliwindram
▴ 10
1
vote
2
replies
2.6k
views
GenomicFeatures::getPromoterSeq error when selecting all promoters sequences (in mice)
GenomicFeatures
getPromoterSeq
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
branislav misovic
▴ 120
4 results • Page
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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