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txdb
•
reset
0
votes
2
replies
1.5k
views
how to get transcript annotation (unique)
txdb
9.7 years ago
KB
▴ 50
9
votes
4
replies
4.3k
views
PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
txdb
txdb.hsapiens.ucsc.hg19.knowngene
txdb.hsapiens.ucsc.hg38.knowngene
org.hs.eg.db
annotation
9.8 years ago
enricoferrero
▴ 680
0
votes
0
replies
1.4k
views
extractUpstreamSeqs with custom genome, no gene_id shown
genomicranges
txdb
genomicfeatures
featureextraction
updated 9.8 years ago by
Martin Morgan
25k • written 9.8 years ago by
wd
▴ 30
4
votes
4
replies
2.6k
views
Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
homo.sapiens
txdb
annotation
updated 9.8 years ago by
Valerie Obenchain
★ 6.8k • written 9.8 years ago by
enricoferrero
▴ 680
0
votes
1
reply
1.7k
views
How to find index position of desired feature_by in TxDb granges?
granges
txdb
genomicfeatures
updated 9.9 years ago by
Martin Morgan
25k • written 9.9 years ago by
vinod.acear
▴ 50
2
votes
2
replies
1.8k
views
How to rename seqlevels style (I, II, III, ...,XVI, Mito to 1,2,3,...16, 17.) in txdb granges?
renameSeqlevels
mapSeqlevels
grangeslist
granges
txdb
9.9 years ago
vinod.acear
▴ 50
1
vote
6
replies
2.6k
views
problem creating txdb object and bsgenome for solanum pennellii
bsgenome
txdb
promoter
updated 10.0 years ago by
Martin Morgan
25k • written 10.0 years ago by
sekawaiwai2006
▴ 20
0
votes
3
replies
2.0k
views
extracting promoter region error for A.thaliana
promoter region
txdb
updated 10.0 years ago by
Martin Morgan
25k • written 10.0 years ago by
sekawaiwai2006
▴ 20
4
votes
7
replies
3.6k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart
genomicfeatures
txdb
biomart
updated 10.2 years ago by
James W. MacDonald
68k • written 10.2 years ago by
vinod.acear
▴ 50
0
votes
4
replies
1.9k
views
threeUTRsByTranscript appears to not work after invoking setter seqlevelsStyle
txdb
threeutrsbytranscript
seqlevelsstyle
seqlevels
10.3 years ago
Robert K. Bradley
▴ 40
0
votes
3
replies
1.8k
views
possible conflict between renameSeqLevels (TxDb) and isActiveSeq (TxDb)
bug
txdb
genomicfeatures
10.4 years ago • updated 10.3 years ago
Robert K. Bradley
▴ 40
0
votes
2
replies
1.4k
views
renamed seqlevels (TxDb) don't persist through a save-load cycle
GenomicFeatures
TxDb
10.4 years ago • updated 10.3 years ago
Robert K. Bradley
▴ 40
2
votes
6
replies
3.3k
views
Working with Arabidopsis Databases
bsgenome
biomart
getPromoterSeq
txdb
10.5 years ago
oliwindram
▴ 10
0
votes
2
replies
2.8k
views
makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf
TxDb
maketxdbfromgff
updated 10.6 years ago by
Hervé Pagès
16k • written 10.6 years ago by
yacine.badis
• 0
8
votes
16
replies
4.1k
views
Setting package name in makeTxDbPackage
genomicfeatures
txdb
updated 10.7 years ago by
Marc Carlson
★ 7.2k • written 10.7 years ago by
Diego Diez
▴ 760
2
votes
2
replies
1.8k
views
Setting genome information on a TxDb object
genomicfeatures
txdb
updated 10.7 years ago by
Hervé Pagès
16k • written 10.7 years ago by
Diego Diez
▴ 760
3
votes
3
replies
4.5k
views
Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
biocinstaller
installation
TxDb
updated 11.0 years ago by
Marc Carlson
★ 7.2k • written 11.0 years ago by
Laurent Gatto
1.6k
67 results • Page
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Answer: Are individual-mouse-based statistics possible in CellChat?
by
ATpoint
★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
Comment: DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
by
ATpoint
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apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Martin Morgan
25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
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43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Benjamin
• 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
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Answer: When to use edgeR or limma
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