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Showing :
GenomicFeatures
•
reset
0
votes
2
replies
118
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 25 days ago by
camilia.savitri
• 0
0
votes
5
replies
242
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 8 weeks ago by
James W. MacDonald
62k • written 8 weeks ago by
teetee
• 0
0
votes
0
replies
100
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
3 months ago
nattzy94
▴ 20
0
votes
2
replies
285
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures
AnnotationHubData
tximeta
updated 4 months ago by
Michael Love
39k • written 4 months ago by
Pratik Mehta
▴ 10
0
votes
4
replies
761
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 8 months ago by
Hervé Pagès
16k • written 8 months ago by
rsnorman
• 0
5
votes
9
replies
751
views
Questions regarding failing tximeta import for swish
swish
fishpond
GenomicFeatures
tximeta
updated 6 months ago by
Michael Love
39k • written 10 months ago by
jvandinter
• 0
0
votes
18
replies
1.7k
views
Indexing FASTA file using RSamtools
Rsamtools
GenomicFeatures
12 months ago • updated 11 months ago
rbenel
▴ 20
3
votes
3
replies
878
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea
GenomicFeatures
updated 9 months ago by
James W. MacDonald
62k • written 13 months ago by
Mikhail Dozmorov
▴ 30
1
vote
2
replies
588
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures
Biostrings
14 months ago
Madza Farias-Virgens
• 0
2
votes
3
replies
1.0k
views
How to get longest isoform
GenomicFeatures
Biostrings
updated 14 months ago by
Hervé Pagès
16k • written 14 months ago by
Madza Farias-Virgens
• 0
1
vote
2
replies
457
views
NAs in my txdb tx_name
GenomicFeatures
Biostrings
14 months ago
Madza Farias-Virgens
• 0
2
votes
2
replies
418
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 14 months ago by
Hervé Pagès
16k • written 15 months ago by
mahshaaban
• 0
5
votes
2
replies
591
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges
sesame
sesameData
GenomicFeatures
16 months ago
Pratik Mehta
▴ 10
0
votes
1
reply
481
views
install GenomicFeatures fail
GenomicFeatures
install
updated 17 months ago by
James W. MacDonald
62k • written 17 months ago by
soda
▴ 80
1
vote
4
replies
638
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
18 months ago
A.J.
▴ 20
1
vote
3
replies
509
views
Can't produce a generegiontrack from my txdb anymore
gviz
GenomicFeatures
18 months ago
A.J.
▴ 20
0
votes
0
replies
344
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures
DEXSeq
18 months ago
Matthias Munz
▴ 10
0
votes
0
replies
410
views
annotatr with custom TxDb
GenomicFeatures
annotatr
genomicFe
21 months ago
António Miguel de Jesus Domingues
▴ 490
0
votes
5
replies
1.4k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures
TxDb
22 months ago
sieminsk
• 0
2
votes
2
replies
899
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF
GenomicFeatures
23 months ago
erhoppe
• 0
0
votes
6
replies
659
views
Splitting TxDb by Strand
GenomicFeatures
TxDb
24 months ago
rproendo
▴ 20
0
votes
3
replies
508
views
Revisiting gene name inclusion in TxDB
Bioconductor
GenomicFeatures
TxDB
updated 15 months ago by
fabian.grammes
• 0 • written 2.2 years ago by
k.vitting.seerup
▴ 120
0
votes
2
replies
1.7k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq
counts
tpm
GenomicFeatures
kallisto
updated 2.3 years ago by
Michael Love
39k • written 2.3 years ago by
m93
• 0
0
votes
1
reply
397
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 24 months ago by
hauken_heyken
▴ 80 • written 2.3 years ago by
lvclark
▴ 10
0
votes
1
reply
2.3k
views
Add gene symbol when making TxDb
txdb
genomicfeatures
updated 2.5 years ago by
James W. MacDonald
62k • written 2.5 years ago by
Jake
▴ 90
3
votes
7
replies
904
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges
GenomicRanges
GenomicFeatures
cdsByOverlaps
DiffBind
updated 2.5 years ago by
James W. MacDonald
62k • written 2.5 years ago by
vanbelj
▴ 20
0
votes
1
reply
641
views
error when creating txdb from gtf
genomicfeatures
makeTxDbFromGRanges
GenomicFeatures
makeTxDbfromGRanges
updated 2.5 years ago by
shepherl
3.4k • written 2.5 years ago by
anze.zupanic
• 0
3
votes
6
replies
870
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb
GenomicFeatures
updated 2.6 years ago by
Martin Morgan
25k • written 2.6 years ago by
Brian Smith
▴ 120
0
votes
1
reply
548
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 2.7 years ago by
James W. MacDonald
62k • written 2.7 years ago by
ribioinfo
▴ 100
0
votes
2
replies
471
views
How to create GRanges for TES
GenomicFeatures
TxDb
CLIP-Seq
updated 2.7 years ago by
Michael Lawrence
11k • written 2.7 years ago by
mar.pieraccioli
▴ 10
0
votes
0
replies
490
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges
genomicfeatures
2.8 years ago
Guandong Shang
▴ 40
0
votes
2
replies
346
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 2.8 years ago by
James W. MacDonald
62k • written 2.8 years ago by
sjmonkley
▴ 40
2
votes
3
replies
975
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb
hg19
ucsc
seqlevel
genomicfeatures
updated 2.8 years ago by
James W. MacDonald
62k • written 2.8 years ago by
foehn
▴ 80
3
votes
4
replies
614
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures
genomicranges
updated 2.9 years ago by
Hervé Pagès
16k • written 2.9 years ago by
Guandong Shang
▴ 40
1
vote
2
replies
480
views
Any possibility to "cache" TxDb object?
GenomicFeatures
TxDb
updated 2.9 years ago by
Steve Lianoglou
13k • written 2.9 years ago by
aush
▴ 40
0
votes
0
replies
472
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures
annotation
gff
GenomicRanges
updated 3.0 years ago by
shepherl
3.4k • written 3.0 years ago by
domenick.braccia
• 0
0
votes
2
replies
563
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart
txdb
makeTxDbFromBiomart
GenomicFeatures
updated 3.0 years ago by
James W. MacDonald
62k • written 3.0 years ago by
ksomi47
• 0
8
votes
12
replies
4.0k
views
Intergenic coordinates with Genomic Feaures
genomicranges
genomicfeatures
iranges
updated 6 months ago by
mehdi
• 0 • written 7.9 years ago by
cookie
▴ 20
2
votes
3
replies
518
views
GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures
GenomicRanges
updated 3.0 years ago by
James W. MacDonald
62k • written 3.0 years ago by
vanbelj
▴ 20
0
votes
3
replies
532
views
Resize exons in transcript to total width
genomicranges
genomicfeatures
updated 3.1 years ago by
Michael Lawrence
11k • written 3.1 years ago by
Jake
▴ 90
0
votes
8
replies
801
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures
GenomicAlignment
GenomicAlignments
exonBy
coverageByTranscript
updated 3.2 years ago by
Hervé Pagès
16k • written 3.2 years ago by
Jiping Wang
▴ 90
2
votes
0
replies
426
views
SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges
GenomicFeatures
grange
distanceToNearest
R
3.2 years ago
rmash
▴ 20
4
votes
3
replies
2.1k
views
TxDb error: external pointer is not valid
software error
GenomicFeatures
3.4 years ago • updated 3.3 years ago
O. William McClung
• 0
0
votes
2
replies
668
views
Error while creating txDb from gtf file
genomicfeatures
3.4 years ago
bioinagesh
• 0
5
votes
5
replies
960
views
threeUTRsByTranscript per GENE
GenomicFeatures
Transcript
gene
threeUTRsByTranscript
updated 23 months ago by
Dario Strbenac
★ 1.5k • written 3.4 years ago by
amgtech
▴ 10
0
votes
1
reply
696
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures
rtracklayer
updated 3.8 years ago by
Hervé Pagès
16k • written 3.8 years ago by
stephane.plaisance
▴ 10
0
votes
0
replies
932
views
error with makeTxDbFromGFF
genomicfeatures
gff
custom genome
makeTxDbFromGFF
makeTxDbFromGRanges
3.8 years ago
xvazquezc
• 0
0
votes
0
replies
461
views
Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 3.9 years ago by
Martin Morgan
25k • written 3.9 years ago by
rodolfobahamonde
• 0
4
votes
5
replies
2.6k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 9 months ago by
Hervé Pagès
16k • written 4.0 years ago by
courtney.stairs
• 0
5
votes
6
replies
1.3k
views
error in makeTxDbFromUCSC
genomicfeatures
R
bioconductor
maketxdbfromucsc
updated 4.0 years ago by
Hervé Pagès
16k • written 4.0 years ago by
alanchenslm
• 0
50 results • Page
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Replies
Comment: mas5calls function doesn't work; mirna40cdf problem
by
James W. MacDonald
62k
Yes. Follow the recommendation in the link that was provided to you by Lori Shepherd.
Comment: mas5calls function doesn't work; mirna40cdf problem
by
Berna
• 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage
by
ayabalbaa1990
• 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object
by
shaimaa
• 0
I used the combat-seq but the deseq complain as its not integer what should i do
Answer: Different summary() and results() values in DeSeq2
by
Basti
▴ 540
summary() tells you the number of genes with low counts, see independant filtering of results in the DESeq2 vignette : https://www.biocondu…
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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