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Showing :
makeTxDbFromGFF
•
reset
2
votes
2
replies
544
views
Problem with MakeTxDbFromGFF
makeTxDbFromGff
9 months ago
stacy.genovese
• 0
3
votes
4
replies
2.1k
views
Saving and retrieving TxDB object
makeTxDBFromGFF
EISA
updated 3.3 years ago by
James W. MacDonald
64k • written 3.3 years ago by
nishanthemje
• 0
0
votes
0
replies
1.4k
views
error with makeTxDbFromGFF
genomicfeatures
gff
custom genome
makeTxDbFromGFF
makeTxDbFromGRanges
4.6 years ago
xvazquezc
• 0
0
votes
1
reply
1.0k
views
Error in .merge_transcript_parts(transcripts)
maketxdbfromgff
5.0 years ago
csijcs
• 0
0
votes
2
replies
2.1k
views
makeTxDbFromGFF errors too many NAs and make.splicings
maketxdbfromgff
limma
updated 5.1 years ago by
Hervé Pagès
16k • written 5.2 years ago by
Karl Lundén
▴ 20
0
votes
1
reply
1.2k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures
txdb
maketxdbfromgff
updated 5.4 years ago by
daniel.vantwisk
▴ 50 • written 5.4 years ago by
marisa.e.miller
• 0
0
votes
0
replies
789
views
Error using the makeTxDbFromGFF
maketxdbfromgff
5.8 years ago
bright602
• 0
0
votes
1
reply
3.5k
views
create a txdb using makeTxDbFromGFF
bioconductor
txdb
maketxdbfromgff
6.0 years ago
Nader.Aryamanesh
• 0
0
votes
3
replies
3.4k
views
makeTxDbFromGFF Error: subscript contains NAs
genomicfeatures
granges
maketxdbfromgff
updated 6.2 years ago by
Hervé Pagès
16k • written 6.4 years ago by
marc_bes
• 0
1
vote
2
replies
966
views
Error while using GenomicFeatures package
genomicfeatures
maketxdbfromgff
updated 6.8 years ago by
Hervé Pagès
16k • written 6.8 years ago by
TFony
▴ 10
3
votes
2
replies
2.0k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures
gtf
maketxdbfromgff
iGenome
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
Marlin
▴ 20
1
vote
2
replies
1.2k
views
mRNA start used instead of gene start in makeTxDbFromGFF
maketxdbfromgff
genomicfeatures
updated 7.6 years ago by
Hervé Pagès
16k • written 7.6 years ago by
TimothéeFlutre
▴ 80
4
votes
2
replies
1.2k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures
txdb
maketxdbfromgff
metadata
updated 7.6 years ago by
Valerie Obenchain
★ 6.8k • written 7.6 years ago by
TimothéeFlutre
▴ 80
0
votes
5
replies
1.5k
views
makeTxDbFromGFF returns empty object
genomicfeatures
txdb
maketxdbfromgff
7.6 years ago
TimothéeFlutre
▴ 80
0
votes
0
replies
871
views
Annotation missing when using makeTxDbFromGFF
makeTxDbFromGFF
7.8 years ago
Udi Landau
▴ 30
8
votes
7
replies
3.1k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 7.9 years ago by
Hervé Pagès
16k • written 7.9 years ago by
gokcen.eraslan
▴ 10
0
votes
7
replies
1.7k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures
maketxdbfromgff
tx_type
gtf
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
Karolin Wiedemann
• 0
0
votes
0
replies
1.1k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures
maketxdbfromgff
tx_type
gtf
8.0 years ago
Karolin Wiedemann
• 0
0
votes
4
replies
1.8k
views
MakeTxDbFromGFF creates empty object
maketxdbfromgff
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
rebecca.halbach
• 0
0
votes
7
replies
2.1k
views
makeTxDbFromGFF yields an empty TxDb
annotation
maketxdbfromgff
genomicfeatures
8.1 years ago
José Luis Lavín
▴ 10
0
votes
2
replies
2.1k
views
makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf
TxDb
maketxdbfromgff
updated 8.4 years ago by
Hervé Pagès
16k • written 8.4 years ago by
yacine.badis
• 0
0
votes
2
replies
1.9k
views
makeTxDbFromGFF not capturing/displaying 'gene' records from GFF3 file.
genomicfeatures
makeTxDbFromGFF
updated 8.6 years ago by
Hervé Pagès
16k • written 8.6 years ago by
pterry
• 0
22 results • Page
1 of 1
Recent ...
Replies
Comment: Result from GSEA for non-model organism not as expected
by
James W. MacDonald
64k
I asked you in a previous thread to **not add comments to old threads** and instead start a new one. Please follow that advice. It's fine i…
Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and
by
James W. MacDonald
64k
This is something you should be able to work out on your own. When you get an error, you have to read it and try to figure out what it mean…
Comment: Subtracting INPUT reads from ChIP read counts.
by
ann-sophie.gironne
• 0
Hi Rory! I'm trying to scale my bigwig files so the visualization on IGV matches what the DiffBind analysis results, being that the sample…
Comment: Ensembl down???
by
James W. MacDonald
64k
Yup, they seem to be down. What exactly are you trying to do? There may be other options.
Answer: Result from GSEA for non-model organism not as expected
by
Aastha Kapoor
• 0
I have a similar issue, I have transcriptome data of an inhouse sequenced bacterial genome. I made the database for that bacteria using mak…
Votes
Comment: Ensembl down???
Answer: Limma/DESeq2 for unbalanced nested design (paired samples)
Result from GSEA for non-model organism not as expected
Comment: DESeq2 estimateSizeFactors iterate takes too long
Answer: DESeq2 estimateSizeFactors iterate takes too long
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