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Showing :
makeTxDBFromGFF
•
reset
2
votes
2
replies
824
views
Problem with MakeTxDbFromGFF
makeTxDbFromGff
14 months ago
stacy.genovese
• 0
3
votes
4
replies
2.6k
views
Saving and retrieving TxDB object
makeTxDBFromGFF
EISA
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
nishanthemje
• 0
0
votes
0
replies
1.5k
views
error with makeTxDbFromGFF
genomicfeatures
gff
custom genome
makeTxDbFromGFF
makeTxDbFromGRanges
5.0 years ago
xvazquezc
• 0
0
votes
1
reply
1.2k
views
Error in .merge_transcript_parts(transcripts)
maketxdbfromgff
5.4 years ago
csijcs
• 0
0
votes
2
replies
2.3k
views
makeTxDbFromGFF errors too many NAs and make.splicings
maketxdbfromgff
limma
updated 5.5 years ago by
Hervé Pagès
16k • written 5.6 years ago by
Karl Lundén
▴ 20
0
votes
1
reply
1.3k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures
txdb
maketxdbfromgff
updated 5.8 years ago by
daniel.vantwisk
▴ 50 • written 5.8 years ago by
marisa.e.miller
• 0
0
votes
0
replies
889
views
Error using the makeTxDbFromGFF
maketxdbfromgff
6.2 years ago
bright602
• 0
0
votes
1
reply
3.9k
views
create a txdb using makeTxDbFromGFF
bioconductor
txdb
maketxdbfromgff
6.4 years ago
Nader.Aryamanesh
• 0
0
votes
3
replies
3.6k
views
makeTxDbFromGFF Error: subscript contains NAs
genomicfeatures
granges
maketxdbfromgff
updated 6.7 years ago by
Hervé Pagès
16k • written 6.8 years ago by
marc_bes
• 0
1
vote
2
replies
1.1k
views
Error while using GenomicFeatures package
genomicfeatures
maketxdbfromgff
updated 7.2 years ago by
Hervé Pagès
16k • written 7.2 years ago by
TFony
▴ 10
3
votes
2
replies
2.2k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures
gtf
maketxdbfromgff
iGenome
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
Marlin
▴ 20
1
vote
2
replies
1.3k
views
mRNA start used instead of gene start in makeTxDbFromGFF
maketxdbfromgff
genomicfeatures
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
TimothéeFlutre
▴ 80
4
votes
2
replies
1.3k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures
txdb
maketxdbfromgff
metadata
updated 8.0 years ago by
Valerie Obenchain
★ 6.8k • written 8.0 years ago by
TimothéeFlutre
▴ 80
0
votes
5
replies
1.6k
views
makeTxDbFromGFF returns empty object
genomicfeatures
txdb
maketxdbfromgff
8.0 years ago
TimothéeFlutre
▴ 80
0
votes
0
replies
942
views
Annotation missing when using makeTxDbFromGFF
makeTxDbFromGFF
8.2 years ago
Udi Landau
▴ 30
8
votes
7
replies
3.4k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 8.3 years ago by
Hervé Pagès
16k • written 8.3 years ago by
gokcen.eraslan
▴ 10
0
votes
7
replies
1.8k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures
maketxdbfromgff
tx_type
gtf
updated 8.4 years ago by
Hervé Pagès
16k • written 8.4 years ago by
Karolin Wiedemann
• 0
0
votes
0
replies
1.2k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures
maketxdbfromgff
tx_type
gtf
8.4 years ago
Karolin Wiedemann
• 0
0
votes
4
replies
2.0k
views
MakeTxDbFromGFF creates empty object
maketxdbfromgff
updated 8.4 years ago by
Hervé Pagès
16k • written 8.4 years ago by
rebecca.halbach
• 0
0
votes
7
replies
2.3k
views
makeTxDbFromGFF yields an empty TxDb
annotation
maketxdbfromgff
genomicfeatures
8.5 years ago
José Luis Lavín
▴ 10
0
votes
2
replies
2.2k
views
makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf
TxDb
maketxdbfromgff
updated 8.8 years ago by
Hervé Pagès
16k • written 8.8 years ago by
yacine.badis
• 0
0
votes
2
replies
2.0k
views
makeTxDbFromGFF not capturing/displaying 'gene' records from GFF3 file.
genomicfeatures
makeTxDbFromGFF
updated 9.0 years ago by
Hervé Pagès
16k • written 9.0 years ago by
pterry
• 0
22 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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