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Showing :
genomicfeatures
•
reset
0
votes
5
replies
105
views
Genomic Features error in TxDbfromGFF
GenomicFeatures
TxDb
15 days ago • updated 14 days ago
sieminsk
• 0
2
votes
2
replies
116
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF
GenomicFeatures
7 weeks ago
erhoppe
• 0
0
votes
6
replies
135
views
Splitting TxDb by Strand
GenomicFeatures
TxDb
10 weeks ago
rproendo
• 0
0
votes
2
replies
96
views
Revisiting gene name inclusion in TxDB
Bioconductor
GenomicFeatures
TxDB
5 months ago
k.vitting.seerup
▴ 100
0
votes
2
replies
150
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq
counts
tpm
GenomicFeatures
kallisto
updated 5 months ago by
Michael Love
32k • written 5 months ago by
m93
• 0
0
votes
1
reply
107
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 8 weeks ago by
hauken_heyken
▴ 80 • written 6 months ago by
lvclark
• 0
0
votes
1
reply
264
views
Add gene symbol when making TxDb
txdb
genomicfeatures
updated 8 months ago by
James W. MacDonald
56k • written 8 months ago by
Jake
▴ 70
3
votes
7
replies
217
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges
GenomicRanges
GenomicFeatures
cdsByOverlaps
DiffBind
updated 8 months ago by
James W. MacDonald
56k • written 8 months ago by
vanbelj
▴ 10
0
votes
1
reply
124
views
error when creating txdb from gtf
genomicfeatures
makeTxDbFromGRanges
GenomicFeatures
makeTxDbfromGRanges
updated 8 months ago by
shepherl
2.6k • written 8 months ago by
anze.zupanic
• 0
3
votes
6
replies
177
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb
GenomicFeatures
updated 9 months ago by
Martin Morgan
25k • written 9 months ago by
Brian Smith
▴ 120
0
votes
1
reply
79
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 10 months ago by
James W. MacDonald
56k • written 10 months ago by
ribioinfo
▴ 90
0
votes
2
replies
116
views
How to create GRanges for TES
GenomicFeatures
TxDb
CLIP-Seq
updated 11 months ago by
Michael Lawrence
11k • written 11 months ago by
mar.pieraccioli
▴ 10
0
votes
0
replies
89
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges
genomicfeatures
11 months ago
shangguandong1996
▴ 20
0
votes
2
replies
84
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 11 months ago by
James W. MacDonald
56k • written 11 months ago by
sjmonkley
▴ 30
2
votes
3
replies
272
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb
hg19
ucsc
seqlevel
genomicfeatures
updated 12 months ago by
James W. MacDonald
56k • written 12 months ago by
foehn
▴ 60
3
votes
4
replies
166
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures
genomicranges
updated 12 months ago by
Hervé Pagès
14k • written 13 months ago by
shangguandong1996
▴ 20
1
vote
2
replies
103
views
Any possibility to "cache" TxDb object?
GenomicFeatures
TxDb
updated 13 months ago by
Steve Lianoglou
13k • written 13 months ago by
aush
▴ 40
0
votes
0
replies
107
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures
annotation
gff
GenomicRanges
updated 14 months ago by
shepherl
2.6k • written 14 months ago by
domenick.braccia
• 0
0
votes
2
replies
89
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart
txdb
makeTxDbFromBiomart
GenomicFeatures
updated 14 months ago by
James W. MacDonald
56k • written 14 months ago by
ksomi47
• 0
6
votes
11
replies
2.8k
views
Intergenic coordinates with Genomic Feaures
genomicranges
genomicfeatures
iranges
updated 14 months ago by
mohancm89
• 0 • written 6.1 years ago by
cookie
▴ 20
2
votes
3
replies
112
views
GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures
GenomicRanges
updated 15 months ago by
James W. MacDonald
56k • written 15 months ago by
vanbelj
▴ 10
0
votes
3
replies
176
views
Resize exons in transcript to total width
genomicranges
genomicfeatures
updated 16 months ago by
Michael Lawrence
11k • written 16 months ago by
Jake
▴ 70
0
votes
8
replies
236
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures
GenomicAlignment
GenomicAlignments
exonBy
coverageByTranscript
updated 17 months ago by
Hervé Pagès
14k • written 17 months ago by
Jiping Wang
▴ 70
0
votes
0
replies
118
views
SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges
GenomicFeatures
grange
distanceToNearest
R
17 months ago
rmash
• 0
4
votes
3
replies
649
views
TxDb error: external pointer is not valid
software error
GenomicFeatures
18 months ago
O. William McClung
• 0
0
votes
2
replies
269
views
Error while creating txDb from gtf file
genomicfeatures
19 months ago
bioinagesh
• 0
3
votes
5
replies
303
views
threeUTRsByTranscript per GENE
GenomicFeatures
Transcript
gene
threeUTRsByTranscript
updated 7 weeks ago by
Dario Strbenac
★ 1.5k • written 19 months ago by
amgtech
• 0
0
votes
1
reply
251
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures
rtracklayer
updated 23 months ago by
Hervé Pagès
14k • written 23 months ago by
stephane.plaisance
▴ 10
0
votes
0
replies
334
views
error with makeTxDbFromGFF
genomicfeatures
gff
custom genome
makeTxDbFromGFF
makeTxDbFromGRanges
24 months ago
xvazquezc
• 0
0
votes
0
replies
205
views
Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 2.1 years ago by
Martin Morgan
25k • written 2.1 years ago by
rodolfobahamonde
• 0
4
votes
3
replies
545
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 2.1 years ago by
Hervé Pagès
14k • written 2.2 years ago by
courtney.stairs
• 0
5
votes
6
replies
576
views
error in makeTxDbFromUCSC
genomicfeatures
R
bioconductor
maketxdbfromucsc
updated 2.2 years ago by
Hervé Pagès
14k • written 2.2 years ago by
alanchenslm
• 0
0
votes
5
replies
308
views
GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures
bug
updated 2.4 years ago by
James W. MacDonald
56k • written 2.4 years ago by
Malcolm Cook
★ 1.5k
1
vote
2
replies
482
views
makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures
makeTxDbFromUCSC
R
2.4 years ago
DMA1
▴ 10
0
votes
2
replies
400
views
Preparation of summarizedExperiment for dexSeq
dexseq
genomicalignments
genomicfeatures
genomicranges
2.5 years ago
A
▴ 40
0
votes
1
reply
374
views
NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 2.5 years ago by
James W. MacDonald
56k • written 2.5 years ago by
zoe.ward
• 0
0
votes
0
replies
411
views
GenomicFeatures: How to extract a gene's upstream region of TSS up to the end position of the flanking (nearby) gene.
genomicranges
genomicfeatures
promoter
upstream_flank
2.6 years ago
Wojeff
• 0
1
vote
8
replies
868
views
Trying to map nucleotide position from a transcript to genomic location
genomicfeatures
mapfromtranscripts
mirna
updated 2.6 years ago by
Valerie Obenchain
★ 6.7k • written 2.6 years ago by
Victoria Perreau
▴ 20
0
votes
1
reply
696
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq
GRanges
GenomicFeatures
2.6 years ago
jerrywu1987
• 0
1
vote
1
reply
428
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures
genomation
genomicranges
methylation
annotation
updated 2.7 years ago by
altuna akalin
▴ 20 • written 2.7 years ago by
alan.g.hudson
• 0
0
votes
1
reply
515
views
getting mouse gene ids from makeTxDbFromUCSC()
GenomicFeatures
makeTxDbFromUCSC
updated 2.7 years ago by
shepherl
2.6k • written 2.7 years ago by
warrena
• 0
0
votes
5
replies
459
views
Custom BSgenome with makeTxDbFromGFF
bsgenome
genomicfeatures
2.7 years ago
michael.weber.1
• 0
0
votes
1
reply
478
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures
txdb
maketxdbfromgff
updated 2.7 years ago by
daniel.vantwisk
▴ 50 • written 2.8 years ago by
marisa.e.miller
• 0
1
vote
1
reply
359
views
makeTxdbFromUCSC fails to download
maketxdbpackagefromucsc
rtracklayer
genomicfeatures
updated 2.8 years ago by
James W. MacDonald
56k • written 2.8 years ago by
lalchungnungabt17
• 0
0
votes
1
reply
1.2k
views
TxDb.Hsapiens.UCSC.hg19.knownGen installation fail - non-zero exit status
software error
package installation
genomicfeatures
updated 2.8 years ago by
Martin Morgan
25k • written 2.8 years ago by
isultan
• 0
3
votes
1
reply
622
views
How does GenomicFeature calculate 3'UTR?
genomicfeatures
annotation
utr
updated 2.8 years ago by
Hervé Pagès
14k • written 2.8 years ago by
hxlei613
• 0
1
vote
3
replies
764
views
GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
genomicfeatures
updated 2.8 years ago by
James W. MacDonald
56k • written 2.8 years ago by
kaur.alasoo
▴ 30
0
votes
1
reply
544
views
TPM and FPKM for lncRNA
GenomicFeatures
TPM
FPKM
lncRNA
2.9 years ago
Ina Hoeschele
▴ 610
0
votes
2
replies
499
views
Cannot get TxDb object using makeTxDbFromUCSC in any table:
software error
genomicfeatures
updated 2.9 years ago by
James W. MacDonald
56k • written 2.9 years ago by
rmendez
• 0
1
vote
1
reply
621
views
installation of "GenomicFeatures"
GenomicFeatures
updated 3.0 years ago by
James W. MacDonald
56k • written 3.0 years ago by
krwyaong.ju
• 0
261 results • Page
1 of 6
Recent ...
Replies
Answer: DepMap copy number
by
Laurent Gatto
1.5k
Hi Danny - sorry for the delay in answering, I hadn't set `depmap` as a tag yet. Yes, that bug has been fixed in the devel version.
Answer: High fold change reported for comparison of samples with zero values in all samp
by
James W. MacDonald
56k
The universal recommendation is to remove all genes with consistently low (or all zero) expression values prior to doing any modeling. It i…
Comment: Sample quality weights for RNA-seq
by
Naomi Altman
★ 6.0k
Thanks Michael. I'll try that. (Limma folks, I'd still love to hear from you.)
Answer: Installation error if message implemented in .Rprofile
by
Mike Smith
★ 4.9k
A similar issue has been reported recently for rhdf5filters (https://github.com/grimbough/rhdf5filters/issues/11) and rhdf5 (https://github…
Comment: Couldn't load org.Hs.eg.db
by
Xulei Huo
• 0
That does not work, i have tried it.
Votes
Answer: TargetsFile. Where it is?
Answer: TargetsFile. Where it is?
Comment: TargetsFile. Where it is?
Comment: Using DESeq2 to identify changing transcriptional activity in a metagenome
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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