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Genomicfeatures
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0
votes
3
replies
209
views
How to get The evolutionary conservation scores for lncRNAs by the phastCons100way.UCSC.hg38 (3.7.1) R package
txdbmaker
GenomicScores
phastCons100way.UCSC.hg38
GenomicFeatures
5 days ago • updated 1 day ago
rania.alanany
• 0
3
votes
2
replies
301
views
ISO a solution to rank-order introns by transcript
GenomicRanges
GenomicFeatures
updated 7 weeks ago by
James W. MacDonald
67k • written 8 weeks ago by
mat149
▴ 80
0
votes
1
reply
542
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene
ensembldb
GenomicFeatures
Mus_musculus
updated 9 months ago by
James W. MacDonald
67k • written 9 months ago by
ramonmassoni
▴ 10
2
votes
1
reply
830
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13
GenomicFeatures
updated 11 months ago by
James W. MacDonald
67k • written 11 months ago by
sarah
• 0
0
votes
1
reply
781
views
How to calculate CDS start and End per transcript from GTF file
dNdScv
GenomicFeatures
TxDb
13 months ago
rohitsatyam102
▴ 20
2
votes
3
replies
3.2k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 14 months ago by
Gordon Smyth
51k • written 14 months ago by
gingergeiger22
• 0
2
votes
2
replies
717
views
Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene
GenomicFeatures
15 months ago
Geert
▴ 10
0
votes
2
replies
1.3k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
17 months ago
gernophil
• 0
1
vote
4
replies
989
views
Submitting BSgenome package for a new assembly
bsgenome
GenomicFeatures
package
updated 17 months ago by
Hervé Pagès
16k • written 18 months ago by
Manish
• 0
1
vote
0
replies
640
views
Make custom Txdb class objects from Txdb
GenomicFeatures
karyoploteR
TxDb.Hsapiens.UCSC.hg19.knownGene
19 months ago
Shreyash
▴ 10
4
votes
8
replies
2.0k
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID
TxDB.Hsapiens.UCSC.hg38.knownGene
locateVariants
GenomicFeatures
VariantAnnotation
20 months ago
davidhillis
• 0
0
votes
2
replies
1.1k
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 22 months ago by
camilia.savitri
• 0
0
votes
5
replies
1.6k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 23 months ago by
James W. MacDonald
67k • written 23 months ago by
teetee
• 0
0
votes
0
replies
607
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
2.1 years ago
nattzy94
▴ 20
0
votes
2
replies
1.4k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures
AnnotationHubData
tximeta
updated 2.2 years ago by
Michael Love
42k • written 2.2 years ago by
Pratik Mehta
▴ 10
0
votes
4
replies
2.5k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 2.5 years ago by
Hervé Pagès
16k • written 2.5 years ago by
rsnorman
• 0
5
votes
9
replies
1.9k
views
Questions regarding failing tximeta import for swish
swish
fishpond
GenomicFeatures
tximeta
updated 2.3 years ago by
Michael Love
42k • written 2.6 years ago by
jvandinter
• 0
0
votes
18
replies
4.3k
views
Indexing FASTA file using RSamtools
Rsamtools
GenomicFeatures
2.8 years ago • updated 2.7 years ago
rbenel
▴ 40
3
votes
3
replies
1.8k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea
GenomicFeatures
updated 2.6 years ago by
James W. MacDonald
67k • written 2.9 years ago by
Mikhail Dozmorov
▴ 30
1
vote
2
replies
1.6k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures
Biostrings
3.0 years ago
Madza Farias-Virgens
• 0
2
votes
3
replies
3.1k
views
How to get longest isoform
GenomicFeatures
Biostrings
updated 3.0 years ago by
Hervé Pagès
16k • written 3.0 years ago by
Madza Farias-Virgens
• 0
1
vote
2
replies
1.2k
views
NAs in my txdb tx_name
GenomicFeatures
Biostrings
3.0 years ago
Madza Farias-Virgens
• 0
2
votes
2
replies
1.1k
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 3.0 years ago by
Hervé Pagès
16k • written 3.0 years ago by
mahshaaban
• 0
5
votes
2
replies
1.3k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges
sesame
sesameData
GenomicFeatures
3.2 years ago
Pratik Mehta
▴ 10
0
votes
1
reply
1.4k
views
install GenomicFeatures fail
GenomicFeatures
install
updated 3.2 years ago by
James W. MacDonald
67k • written 3.2 years ago by
soda
▴ 80
1
vote
4
replies
1.8k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
3.3 years ago
A.J.
▴ 20
1
vote
3
replies
1.3k
views
Can't produce a generegiontrack from my txdb anymore
gviz
GenomicFeatures
3.3 years ago
A.J.
▴ 20
1
vote
0
replies
1.2k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures
DEXSeq
3.3 years ago
Matthias Munz
▴ 20
0
votes
0
replies
959
views
annotatr with custom TxDb
GenomicFeatures
annotatr
genomicFe
3.6 years ago
António Miguel de Jesus Domingues
▴ 510
0
votes
5
replies
3.2k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures
TxDb
3.6 years ago
sieminsk
• 0
2
votes
2
replies
1.9k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF
GenomicFeatures
3.7 years ago
erhoppe
• 0
0
votes
6
replies
1.5k
views
Splitting TxDb by Strand
GenomicFeatures
TxDb
3.8 years ago
rproendo
▴ 30
0
votes
3
replies
1.4k
views
Revisiting gene name inclusion in TxDB
Bioconductor
GenomicFeatures
TxDB
updated 3.1 years ago by
fabian.grammes
• 0 • written 4.0 years ago by
k.vitting.seerup
▴ 120
0
votes
2
replies
3.6k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq
counts
tpm
GenomicFeatures
kallisto
updated 4.1 years ago by
Michael Love
42k • written 4.1 years ago by
m93
• 0
0
votes
1
reply
813
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.8 years ago by
hauken_heyken
▴ 80 • written 4.1 years ago by
lvclark
▴ 10
0
votes
1
reply
5.2k
views
Add gene symbol when making TxDb
txdb
genomicfeatures
updated 4.3 years ago by
James W. MacDonald
67k • written 4.3 years ago by
Jake
▴ 90
3
votes
7
replies
1.7k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges
GenomicRanges
GenomicFeatures
cdsByOverlaps
DiffBind
updated 4.3 years ago by
James W. MacDonald
67k • written 4.3 years ago by
vanbelj
▴ 30
0
votes
1
reply
1.4k
views
error when creating txdb from gtf
genomicfeatures
makeTxDbFromGRanges
GenomicFeatures
makeTxDbfromGRanges
updated 4.3 years ago by
shepherl
4.1k • written 4.3 years ago by
anze.zupanic
• 0
3
votes
6
replies
2.4k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb
GenomicFeatures
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
Brian Smith
▴ 120
0
votes
1
reply
1.4k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 4.5 years ago by
James W. MacDonald
67k • written 4.5 years ago by
ribioinfo
▴ 100
0
votes
2
replies
1.2k
views
How to create GRanges for TES
GenomicFeatures
TxDb
CLIP-Seq
updated 4.5 years ago by
Michael Lawrence
★ 11k • written 4.5 years ago by
mar.pieraccioli
▴ 10
0
votes
0
replies
1.1k
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges
genomicfeatures
4.6 years ago
Guandong Shang
▴ 40
0
votes
2
replies
973
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.6 years ago by
James W. MacDonald
67k • written 4.6 years ago by
sjmonkley
▴ 40
2
votes
3
replies
2.0k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb
hg19
ucsc
seqlevel
genomicfeatures
updated 4.6 years ago by
James W. MacDonald
67k • written 4.6 years ago by
foehn
▴ 100
3
votes
4
replies
1.3k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures
genomicranges
updated 4.7 years ago by
Hervé Pagès
16k • written 4.7 years ago by
Guandong Shang
▴ 40
1
vote
2
replies
1.1k
views
Any possibility to "cache" TxDb object?
GenomicFeatures
TxDb
updated 4.7 years ago by
Steve Lianoglou
★ 13k • written 4.7 years ago by
aush
▴ 40
0
votes
0
replies
1.1k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures
annotation
gff
GenomicRanges
updated 4.8 years ago by
shepherl
4.1k • written 4.8 years ago by
domenick.braccia
• 0
0
votes
2
replies
1.1k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart
txdb
makeTxDbFromBiomart
GenomicFeatures
updated 4.8 years ago by
James W. MacDonald
67k • written 4.8 years ago by
ksomi47
• 0
8
votes
12
replies
6.1k
views
Intergenic coordinates with Genomic Feaures
genomicranges
genomicfeatures
iranges
updated 2.4 years ago by
mehdi
• 0 • written 9.7 years ago by
cookie
▴ 20
2
votes
3
replies
1.4k
views
GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures
GenomicRanges
updated 4.9 years ago by
James W. MacDonald
67k • written 4.9 years ago by
vanbelj
▴ 30
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