Showing : GenomicFeatures • reset
2
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3
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379
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Guitar R package requires update due to dependency GenomicFeatures
GenomicFeatures Guitar txdbmaker GenomicRanges
written 15 days ago by ▴ 10
4
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9
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3.1k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 11 months ago by ★ 3.4k • written 13 months ago by ▴ 20
0
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3
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718
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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
14 months ago • updated 13 months ago rania.alanany • 0
3
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3
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870
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
15 months ago • updated 13 months ago mat149 ▴ 80
0
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2
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1.1k
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Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
written 23 months ago by ▴ 10
2
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1
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1.5k
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Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
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1
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1.4k
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How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
2.2 years ago rohitsatyam102 ▴ 20
2
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3
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5.1k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
2
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2
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1.2k
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Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
2.4 years ago Geert ▴ 10
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2
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2.0k
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What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
2.6 years ago gernophil • 0
1
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4
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1.4k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
1
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0
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952
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
2.7 years ago Shreyash ▴ 10
4
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8
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3.2k
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
2.8 years ago davidhillis • 0
0
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2
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1.6k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 3.0 years ago by • 0
0
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5
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2.0k
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Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
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0
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918
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
3.2 years ago nattzy94 ▴ 20
0
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2
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1.9k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
0
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4
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3.1k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
5
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9
replies
2.6k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.4 years ago by 43k • written 3.8 years ago by • 0
0
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18
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5.9k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
3.9 years ago rbenel ▴ 50
3
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3
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2.2k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 3.7 years ago by 68k • written 4.1 years ago by ▴ 30
1
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2
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2.1k
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
4.2 years ago Madza Farias-Virgens • 0
2
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3
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4.0k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 4.2 years ago by 16k • written 4.2 years ago by • 0
1
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2
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1.6k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
4.2 years ago Madza Farias-Virgens • 0
2
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2
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1.4k
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 4.2 years ago by 16k • written 4.2 years ago by • 0
5
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2
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1.7k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.3 years ago Pratik Mehta ▴ 10
0
votes
1
reply
1.8k
views
install GenomicFeatures fail
GenomicFeatures install
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 80
1
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4
replies
2.3k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
4.4 years ago A.J. ▴ 20
1
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3
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1.8k
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Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
4.4 years ago A.J. ▴ 20
1
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0
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1.7k
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
4.5 years ago Matthias Munz ▴ 20
0
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0
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1.3k
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
4.7 years ago António Miguel de Jesus Domingues ▴ 510
0
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5
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3.9k
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
4.8 years ago sieminsk • 0
2
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2
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2.3k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
4.9 years ago erhoppe • 0
0
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6
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2.0k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
4.9 years ago rproendo ▴ 30
0
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3
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1.7k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 4.2 years ago by • 0 • written 5.2 years ago by ▴ 120
0
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2
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4.4k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
0
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1
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1.1k
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 4.9 years ago by ▴ 80 • written 5.3 years ago by ▴ 10
0
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1
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6.0k
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Add gene symbol when making TxDb
txdb genomicfeatures
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 90
3
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7
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2.3k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 30
0
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1
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1.8k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 5.5 years ago by 4.3k • written 5.5 years ago by • 0
3
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6
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3.3k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 120
0
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1
reply
1.9k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 100
0
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2
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1.6k
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How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 5.7 years ago by ★ 11k • written 5.7 years ago by ▴ 10
0
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0
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1.4k
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
5.7 years ago Guandong Shang ▴ 40
0
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2
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1.2k
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 40
2
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3
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2.5k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 100
3
votes
4
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1.7k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 40
1
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2
replies
1.4k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 5.9 years ago by ★ 13k • written 5.9 years ago by ▴ 40
0
votes
0
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1.4k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 5.9 years ago by 4.3k • written 5.9 years ago by • 0
0
votes
2
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1.4k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
292 results • Page 1 of 6
Recent ...
Replies
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
Awards • All
Commentator to James W. MacDonald 68k
Great Question to fl ▴ 20
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
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