Showing : genomicfeatures • reset
4
votes
9
replies
2.1k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 28 days ago by ★ 3.4k • written 9 weeks ago by ▴ 20
0
votes
3
replies
349
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
3 months ago rania.alanany • 0
3
votes
3
replies
487
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
4 months ago • updated 9 weeks ago mat149 ▴ 80
0
votes
1
reply
656
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 12 months ago by 68k • written 12 months ago by ▴ 10
2
votes
1
reply
1.0k
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
1
reply
919
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
16 months ago rohitsatyam102 ▴ 20
2
votes
3
replies
3.9k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 17 months ago by 52k • written 17 months ago by • 0
2
votes
2
replies
798
views
Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
18 months ago Geert ▴ 10
0
votes
2
replies
1.5k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
20 months ago gernophil • 0
1
vote
4
replies
1.1k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 21 months ago by 16k • written 21 months ago by • 0
1
vote
0
replies
722
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
22 months ago Shreyash ▴ 10
4
votes
8
replies
2.3k
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
23 months ago davidhillis • 0
0
votes
2
replies
1.3k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.1 years ago by • 0
0
votes
5
replies
1.7k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
0
replies
661
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
2.3 years ago nattzy94 ▴ 20
0
votes
2
replies
1.5k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
0
votes
4
replies
2.7k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 2.7 years ago by 16k • written 2.8 years ago by • 0
5
votes
9
replies
2.0k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 2.6 years ago by 43k • written 2.9 years ago by • 0
0
votes
18
replies
4.6k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
3.1 years ago • updated 3.0 years ago rbenel ▴ 40
3
votes
3
replies
1.9k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 2.8 years ago by 68k • written 3.2 years ago by ▴ 30
1
vote
2
replies
1.7k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.3 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.3k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.3 years ago by 16k • written 3.3 years ago by • 0
1
vote
2
replies
1.3k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.3 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 3.3 years ago by 16k • written 3.3 years ago by • 0
5
votes
2
replies
1.4k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.4 years ago Pratik Mehta ▴ 10
0
votes
1
reply
1.6k
views
install GenomicFeatures fail
GenomicFeatures install
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 80
1
vote
4
replies
1.9k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
3.6 years ago • updated 3.5 years ago A.J. ▴ 20
1
vote
3
replies
1.4k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
3.6 years ago A.J. ▴ 20
1
vote
0
replies
1.4k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.6 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.0k
views
annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.8 years ago António Miguel de Jesus Domingues ▴ 510
0
votes
5
replies
3.4k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.9 years ago sieminsk • 0
2
votes
2
replies
2.0k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
4.0 years ago erhoppe • 0
0
votes
6
replies
1.6k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
4.1 years ago rproendo ▴ 30
0
votes
3
replies
1.4k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 3.3 years ago by • 0 • written 4.3 years ago by ▴ 120
0
votes
2
replies
3.8k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
1
reply
867
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 4.0 years ago by ▴ 80 • written 4.4 years ago by ▴ 10
0
votes
1
reply
5.4k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 90
3
votes
7
replies
1.8k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 30
0
votes
1
reply
1.6k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 4.6 years ago by 4.1k • written 4.6 years ago by • 0
3
votes
6
replies
2.6k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 4.6 years ago by 25k • written 4.6 years ago by ▴ 120
0
votes
1
reply
1.6k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 100
0
votes
2
replies
1.3k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.8 years ago by ★ 11k • written 4.8 years ago by ▴ 10
0
votes
0
replies
1.2k
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
4.8 years ago Guandong Shang ▴ 40
0
votes
2
replies
1.0k
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 40
2
votes
3
replies
2.1k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 100
3
votes
4
replies
1.4k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 4.9 years ago by 16k • written 4.9 years ago by ▴ 40
1
vote
2
replies
1.2k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 5.0 years ago by ★ 13k • written 5.0 years ago by ▴ 40
0
votes
0
replies
1.2k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 5.0 years ago by 4.1k • written 5.0 years ago by • 0
0
votes
2
replies
1.2k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
8
votes
12
replies
6.3k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.6 years ago by • 0 • written 9.9 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
Awards • All
Popular Question to leakerb • 0
Popular Question to Mark Dunning ★ 1.1k
Popular Question to shepherl 4.1k
Popular Question to Hugo Varet ▴ 80
Popular Question to Fred Hutch (Recruiting) ▴ 40
Locations • All
United States, 1 hour ago
WEHI, Melbourne, Australia, 3 hours ago
Seattle, WA, United States, 3 hours ago
United States, 4 hours ago
Türkiye, 6 hours ago
Traffic: 520 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