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Showing :
maketxdbfromgff
•
reset
2
votes
2
replies
827
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 7.5 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
1.7k
views
makeTxDbFromGFF returns empty object
genomicfeatures
txdb
maketxdbfromgff
8.0 years ago
TimothéeFlutre
▴ 80
0
votes
0
replies
943
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: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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