Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
TxDb
•
reset
0
votes
1
reply
439
views
How to calculate CDS start and End per transcript from GTF file
dNdScv
GenomicFeatures
TxDb
5 months ago
rohitsatyam102
▴ 20
2
votes
5
replies
671
views
bambu output
txdb
bambu
updated 10 months ago by
andre_sim
▴ 20 • written 10 months ago by
camilia.savitri
• 0
0
votes
0
replies
576
views
Identify accepted columns in TxDb objects
TxDb
15 months ago
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
558
views
TxDb conversion of transcript id to gene id
TxDb.Sscrofa.UCSC.susScr11.refGene
TxDb
txi
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Luke
• 0
3
votes
5
replies
1.8k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges
split
chromosome
TxDb
updated 2.4 years ago by
Hervé Pagès
16k • written 2.4 years ago by
jon.klonowski
▴ 40
5
votes
6
replies
2.0k
views
NA transcript values in my Txdb
GFF
txdb
updated 2.4 years ago by
James W. MacDonald
65k • written 2.5 years ago by
A.J.
▴ 20
1
vote
7
replies
2.1k
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb
R
annotatation
2.8 years ago
pegah.taklifi
▴ 30
0
votes
5
replies
2.7k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures
TxDb
3.1 years ago
sieminsk
• 0
0
votes
6
replies
1.2k
views
Splitting TxDb by Strand
GenomicFeatures
TxDb
3.2 years ago
rproendo
▴ 20
0
votes
3
replies
1.0k
views
Revisiting gene name inclusion in TxDB
Bioconductor
GenomicFeatures
TxDB
updated 2.5 years ago by
fabian.grammes
• 0 • written 3.5 years ago by
k.vitting.seerup
▴ 120
0
votes
1
reply
4.4k
views
Add gene symbol when making TxDb
txdb
genomicfeatures
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
Jake
▴ 90
0
votes
5
replies
1.4k
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
Charlotte
• 0
3
votes
6
replies
1.9k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb
GenomicFeatures
updated 3.8 years ago by
Martin Morgan
25k • written 3.8 years ago by
Brian Smith
▴ 120
3
votes
6
replies
1.1k
views
Extremely big genes in annotation TxDb packages
annotation
txdb
AnnotationData
Genetics
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
epibio
▴ 10
0
votes
2
replies
805
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation
software
TxDb
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
AmalAbdel-Aziz
• 0
0
votes
0
replies
844
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker
TxDb
getpromoters
software error
3.9 years ago
hfyuan2016
• 0
0
votes
2
replies
1.0k
views
How to create GRanges for TES
GenomicFeatures
TxDb
CLIP-Seq
updated 3.9 years ago by
Michael Lawrence
★ 11k • written 3.9 years ago by
mar.pieraccioli
▴ 10
1
vote
2
replies
876
views
Any possibility to "cache" TxDb object?
GenomicFeatures
TxDb
updated 4.1 years ago by
Steve Lianoglou
★ 13k • written 4.1 years ago by
aush
▴ 40
0
votes
2
replies
972
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart
txdb
makeTxDbFromBiomart
GenomicFeatures
updated 4.2 years ago by
James W. MacDonald
65k • written 4.2 years ago by
ksomi47
• 0
0
votes
5
replies
1.9k
views
Changing Gene ID annotation style - working with Salmon output [NM...] and resulting count files are numeric-only IDs
tximport
Gene IDs
txdb
RefSeq
Salmon
updated 4.2 years ago by
Michael Love
41k • written 4.2 years ago by
holmkn
• 0
6
votes
5
replies
1.0k
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb
annotation
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 4.3 years ago by
shepherl
3.8k • written 4.3 years ago by
bernatgel
▴ 150
6
votes
4
replies
2.6k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb
genome
exons
updated 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
Bogdan
▴ 670
2
votes
5
replies
2.1k
views
Warning in makeTxDbFromGFF
txdb
updated 3.1 years ago by
Hervé Pagès
16k • written 4.9 years ago by
weir
▴ 10
2
votes
1
reply
879
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb
GRanges
BSGenome
variant annotation
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
jacorvar
▴ 40
3
votes
2
replies
1.7k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges
ChIPseeker
annotatePeak
TxDb
EnsDb
updated 5.2 years ago by
Johannes Rainer
★ 2.0k • written 5.2 years ago by
foehn
▴ 100
2
votes
4
replies
1.4k
views
Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.knownGene: incorrect number of exons and overlapping exons
txdb
txdb.hsapiens.ucsc.hg19.knowngene
granges
exons
ucsc
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
olavur
▴ 10
0
votes
3
replies
1.4k
views
Error in makeTxDbFromBiomart
software error
txdb
maketxdbfrombiomart
5.5 years ago
katie_emelianova
• 0
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
1
reply
1.0k
views
TxDb basic question
txdb
TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 5.8 years ago by
daniel.vantwisk
▴ 50 • written 5.8 years ago by
Brian Smith
▴ 120
0
votes
4
replies
1.7k
views
Merging each element of a list of Genomic range
txdb
granges
cds
orf
R
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
q.thomas
• 0
0
votes
1
reply
1.0k
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures
rnaseq
txdb
6.1 years ago
lucasmacielbiotec
• 0
1
vote
5
replies
1.9k
views
Extract genomic features from a TxDb-like object
TxDB
genomicfeatures
promoter
getpromoterseq
updated 6.1 years ago by
Hervé Pagès
16k • written 6.1 years ago by
rbenel
▴ 40
0
votes
1
reply
3.9k
views
create a txdb using makeTxDbFromGFF
bioconductor
txdb
maketxdbfromgff
6.4 years ago
Nader.Aryamanesh
• 0
2
votes
4
replies
2.1k
views
possible Rtracklayer issue: TxDb errors in GenomicFeatures package-- cannot load TxDb with standard params from UCSC (issue began last night)
genomicfeatures
txdb
maketxdbfromucsc
maketxdbfrombiomart
rtracklayer
updated 6.4 years ago by
Michael Lawrence
★ 11k • written 6.4 years ago by
james.dalgleish
▴ 30
2
votes
2
replies
4.4k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb
gff3
polycistronic transcript
6.5 years ago
Piotr Gawronski
• 0
0
votes
4
replies
1.6k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB
genomicranges
genomicfeatures
updated 6.5 years ago by
Hervé Pagès
16k • written 6.5 years ago by
oolongoni
▴ 10
0
votes
0
replies
1.3k
views
News:
OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb
txdb
bioconductor
annotation
annotationhub
News
6.5 years ago
shepherl
3.8k
0
votes
2
replies
1.5k
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb
txdb.hsapiens.ucsc.hg19.knowngene
gviz
updated 6.5 years ago by
James W. MacDonald
65k • written 6.5 years ago by
izzy.yichao.cai
▴ 10
4
votes
5
replies
1.5k
views
R session crash with SGSeq::convertToTxFeatures
crash
SGSeq
TxDb
makeTxDbFromBiomart
TxFeatures
updated 6.6 years ago by
Leonard Goldstein
▴ 180 • written 6.6 years ago by
oolongoni
▴ 10
0
votes
2
replies
2.0k
views
add annotation features to BSgenome or txdb package
bsgenome
txdb
annotation
orgdb
6.8 years ago • updated 6.7 years ago
Didi
▴ 10
0
votes
2
replies
1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment
TxDb
gtf
genomicfeatures
updated 6.8 years ago by
Michael Love
41k • written 6.8 years ago by
filipeje
• 0
0
votes
1
reply
1.2k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures
txdb
canis familiaris
rna-seq
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
jggomeza
• 0
5
votes
7
replies
1.9k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb
genomicfeatures
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
Chao-Jen Wong
▴ 40
2
votes
1
reply
1.1k
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures
txdb
updated 7.4 years ago by
James W. MacDonald
65k • written 7.4 years ago by
gtho123
▴ 40
0
votes
2
replies
1.3k
views
Error in TxDb mm10 coordinates?
txdb
txdb.mmusculus.ucsc.mm10.knowngene
updated 7.4 years ago by
James W. MacDonald
65k • written 7.4 years ago by
Mark
▴ 10
3
votes
3
replies
1.3k
views
Genes found on particular chromosome using two methods in TxDb.Hsapiens.UCSC.hg19.knownGene were not identical
txdb.hsapiens.ucsc.hg19.knowngene
txdb
updated 7.7 years ago by
Martin Morgan
25k • written 7.7 years ago by
li lilingdu
▴ 450
1
vote
2
replies
2.5k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures
txdb
makeTxDbFromGRanges
updated 7.8 years ago by
Hervé Pagès
16k • written 7.8 years ago by
Guido Hooiveld
★ 3.9k
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
2
replies
1.2k
views
how to get transcript annotation (unique)
txdb
8.0 years ago
KB
▴ 50
50 results • Page
1 of 1
Recent ...
Replies
Comment: Different Shrunk Log2FC according with reference
by
Michael Love
41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Votes
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Awards
• All
Popular Question
to
Bine
▴ 40
Scholar
to
ATpoint
★ 4.0k
Popular Question
to
Gordon Smyth
50k
Popular Question
to
i.sudbery
▴ 40
Scholar
to
Michael Love
41k
Locations
• All
United States,
1 minute ago
Belgium,
8 minutes ago
France,
17 minutes ago
Germany,
23 minutes ago
Canada,
28 minutes ago
Traffic: 838 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6