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Showing :
makeTxDbFromGff
•
reset
2
votes
3
replies
1.8k
views
Problem with MakeTxDbFromGFF
makeTxDbFromGff
written 2.6 years ago by
stacy.genovese
• 0
3
votes
4
replies
4.0k
views
Saving and retrieving TxDB object
makeTxDBFromGFF
EISA
updated 5.2 years ago by
James W. MacDonald
68k • written 5.2 years ago by
nishanthemje
• 0
0
votes
0
replies
1.9k
views
error with makeTxDbFromGFF
genomicfeatures
gff
custom genome
makeTxDbFromGFF
makeTxDbFromGRanges
6.5 years ago
xvazquezc
• 0
0
votes
1
reply
1.6k
views
Error in .merge_transcript_parts(transcripts)
maketxdbfromgff
6.9 years ago
csijcs
• 0
0
votes
2
replies
2.8k
views
makeTxDbFromGFF errors too many NAs and make.splicings
maketxdbfromgff
limma
updated 7.0 years ago by
Hervé Pagès
16k • written 7.1 years ago by
Karl Lundén
▴ 20
0
votes
1
reply
1.8k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures
txdb
maketxdbfromgff
updated 7.3 years ago by
daniel.vantwisk
▴ 50 • written 7.3 years ago by
marisa.e.miller
• 0
0
votes
0
replies
1.2k
views
Error using the makeTxDbFromGFF
maketxdbfromgff
7.7 years ago
bright602
• 0
0
votes
1
reply
4.6k
views
create a txdb using makeTxDbFromGFF
bioconductor
txdb
maketxdbfromgff
7.9 years ago
Nader.Aryamanesh
• 0
0
votes
3
replies
4.4k
views
makeTxDbFromGFF Error: subscript contains NAs
genomicfeatures
granges
maketxdbfromgff
updated 8.1 years ago by
Hervé Pagès
16k • written 8.3 years ago by
marc_bes
• 0
1
vote
2
replies
1.4k
views
Error while using GenomicFeatures package
genomicfeatures
maketxdbfromgff
updated 8.7 years ago by
Hervé Pagès
16k • written 8.7 years ago by
TFony
▴ 10
3
votes
2
replies
2.7k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures
gtf
maketxdbfromgff
iGenome
updated 8.9 years ago by
Martin Morgan
25k • written 8.9 years ago by
Marlin
▴ 20
1
vote
2
replies
1.7k
views
mRNA start used instead of gene start in makeTxDbFromGFF
maketxdbfromgff
genomicfeatures
updated 9.5 years ago by
Hervé Pagès
16k • written 9.5 years ago by
TimothéeFlutre
▴ 80
4
votes
2
replies
1.7k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures
txdb
maketxdbfromgff
metadata
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
TimothéeFlutre
▴ 80
0
votes
5
replies
2.2k
views
makeTxDbFromGFF returns empty object
genomicfeatures
txdb
maketxdbfromgff
9.5 years ago
TimothéeFlutre
▴ 80
0
votes
0
replies
1.2k
views
Annotation missing when using makeTxDbFromGFF
makeTxDbFromGFF
9.7 years ago
Udi Landau
▴ 30
8
votes
7
replies
4.5k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 9.8 years ago by
Hervé Pagès
16k • written 9.8 years ago by
gokcen.eraslan
▴ 10
0
votes
7
replies
2.4k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures
maketxdbfromgff
tx_type
gtf
updated 9.9 years ago by
Hervé Pagès
16k • written 9.9 years ago by
Karolin Wiedemann
• 0
0
votes
0
replies
1.4k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures
maketxdbfromgff
tx_type
gtf
9.9 years ago
Karolin Wiedemann
• 0
0
votes
4
replies
2.4k
views
MakeTxDbFromGFF creates empty object
maketxdbfromgff
updated 9.9 years ago by
Hervé Pagès
16k • written 9.9 years ago by
rebecca.halbach
• 0
0
votes
7
replies
2.9k
views
makeTxDbFromGFF yields an empty TxDb
annotation
maketxdbfromgff
genomicfeatures
10.0 years ago
José Luis Lavín
▴ 10
0
votes
2
replies
2.7k
views
makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf
TxDb
maketxdbfromgff
updated 10.3 years ago by
Hervé Pagès
16k • written 10.3 years ago by
yacine.badis
• 0
0
votes
2
replies
2.5k
views
makeTxDbFromGFF not capturing/displaying 'gene' records from GFF3 file.
genomicfeatures
makeTxDbFromGFF
updated 10.5 years ago by
Hervé Pagès
16k • written 10.5 years ago by
pterry
• 0
22 results • Page
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Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Votes
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
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