Showing : GenomicFeatures • reset
4
votes
9
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2.9k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 9 months ago by ★ 3.4k • written 10 months ago by ▴ 20
0
votes
3
replies
634
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
11 months ago rania.alanany • 0
3
votes
3
replies
790
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
13 months ago • updated 10 months ago mat149 ▴ 80
0
votes
2
replies
978
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
written 21 months ago by ▴ 10
2
votes
1
reply
1.4k
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 22 months ago by 68k • written 22 months ago by • 0
0
votes
1
reply
1.3k
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
2.0 years ago rohitsatyam102 ▴ 20
2
votes
3
replies
4.8k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
2
votes
2
replies
1.1k
views
Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
2.3 years ago • updated 2.2 years ago Geert ▴ 10
0
votes
2
replies
1.9k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
2.4 years ago gernophil • 0
1
vote
4
replies
1.3k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
1
vote
0
replies
891
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
2.5 years ago Shreyash ▴ 10
4
votes
8
replies
2.9k
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
2.6 years ago davidhillis • 0
0
votes
2
replies
1.5k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.8 years ago by • 0
0
votes
5
replies
1.9k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
0
replies
848
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
3.0 years ago nattzy94 ▴ 20
0
votes
2
replies
1.8k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
0
votes
4
replies
3.0k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 3.4 years ago by 16k • written 3.5 years ago by • 0
5
votes
9
replies
2.4k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.3 years ago by 43k • written 3.6 years ago by • 0
0
votes
18
replies
5.6k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
3.8 years ago • updated 3.7 years ago rbenel ▴ 50
3
votes
3
replies
2.1k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 3.5 years ago by 68k • written 3.9 years ago by ▴ 30
1
vote
2
replies
2.0k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
4.0 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.8k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
1
vote
2
replies
1.6k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
4.0 years ago Madza Farias-Virgens • 0
2
votes
2
replies
1.3k
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
5
votes
2
replies
1.6k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.1 years ago Pratik Mehta ▴ 10
0
votes
1
reply
1.8k
views
install GenomicFeatures fail
GenomicFeatures install
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 80
1
vote
4
replies
2.2k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
4.2 years ago A.J. ▴ 20
1
vote
3
replies
1.7k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
4.3 years ago • updated 4.2 years ago A.J. ▴ 20
1
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0
replies
1.5k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
4.3 years ago Matthias Munz ▴ 20
0
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0
replies
1.2k
views
annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
4.5 years ago António Miguel de Jesus Domingues ▴ 510
0
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5
replies
3.8k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
4.6 years ago sieminsk • 0
2
votes
2
replies
2.2k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
4.7 years ago erhoppe • 0
0
votes
6
replies
1.8k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
4.7 years ago rproendo ▴ 30
0
votes
3
replies
1.6k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 4.0 years ago by • 0 • written 5.0 years ago by ▴ 120
0
votes
2
replies
4.2k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
votes
1
reply
990
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 4.7 years ago by ▴ 80 • written 5.1 years ago by ▴ 10
0
votes
1
reply
5.9k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 90
3
votes
7
replies
2.2k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 5.2 years ago by 68k • written 5.2 years ago by ▴ 30
0
votes
1
reply
1.8k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 5.3 years ago by 4.2k • written 5.3 years ago by • 0
3
votes
6
replies
3.1k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 120
0
votes
1
reply
1.8k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 100
0
votes
2
replies
1.5k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 5.5 years ago by ★ 11k • written 5.5 years ago by ▴ 10
0
votes
0
replies
1.3k
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
5.5 years ago Guandong Shang ▴ 40
0
votes
2
replies
1.2k
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 40
2
votes
3
replies
2.4k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 100
3
votes
4
replies
1.6k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 40
1
vote
2
replies
1.3k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 40
0
votes
0
replies
1.4k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 5.7 years ago by 4.2k • written 5.7 years ago by • 0
0
votes
2
replies
1.3k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
8
votes
12
replies
6.9k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 3.3 years ago by • 0 • written 10.6 years ago by ▴ 20
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Comment: "Watched Tags" are being erased rather than updated by dipakosikotes • 0
Possibly a combination: some change in the forum software that affects some accounts/configurations but not all [unblocked games][1] […
Answer: EuroBioC2023 abstract submission is open! by Hao • 0
It's obvious that the blogger hought on details. It is not only easy to read but also makes the content more rich and interesting.[1v1 …
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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