Showing : GenomicFeatures • reset
5
votes
4
replies
2.1k
views
GenomicFeatures and custom genomes?
genomicfeatures
updated 8.0 years ago by 16k • written 8.1 years ago by ▴ 10
3
votes
10
replies
4.8k
views
CDS phase information missing from GenomicFeatures
GenomicFeatures phase gene models GFF
updated 8.1 years ago by 16k • written 8.1 years ago by ▴ 10
2
votes
4
replies
5.6k
views
Gene Size using GenomicFeatures
genomicfeatures gene size gene length
updated 8.1 years ago by 16k • written 8.1 years ago by • 0
2
votes
2
replies
5.4k
views
Could not find function "makeTranscriptDbFromGFF"
GenomicFeatures makeTranscriptDbFromGFF gff annotation
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 20
8
votes
6
replies
2.6k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 20
4
votes
3
replies
5.0k
views
subsetting GRanges object based on gene IDs
genomicranges genomicfeatures granges subsetting
8.2 years ago Assa Yeroslaviz ★ 1.5k
0
votes
3
replies
4.5k
views
makeTxDbFromGFF Error: subscript contains NAs
genomicfeatures granges maketxdbfromgff
updated 8.2 years ago by 16k • written 8.3 years ago by • 0
3
votes
13
replies
3.6k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder genomicfeatures genomicranges
updated 8.2 years ago by ★ 1.1k • written 8.2 years ago by ▴ 20
0
votes
3
replies
2.2k
views
errors with makeTxDbFromBiomart
biomart genomicfeatures maketxdbfrombiomart ensembldb ensDbFromGtf
updated 8.3 years ago by ★ 2.1k • written 8.3 years ago by • 0
0
votes
2
replies
1.8k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
5
votes
4
replies
3.4k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 8.3 years ago by ★ 1.6k • written 8.3 years ago by ★ 3.4k
0
votes
1
reply
786
views
Issues with .extractEnsemblReleaseFromDbVersion() and get_organism_from_Ensembl_Mart_dataset()
genomicfeatures
updated 8.4 years ago by 16k • written 8.4 years ago by ▴ 10
1
vote
8
replies
4.0k
views
GenomicFeatures package ERROR
software error genomicfeatures
updated 8.4 years ago by ★ 11k • written 9.9 years ago by • 0
0
votes
1
reply
1.4k
views
Genomicfeatures- Error: Image not found, dynamic loading, reputed error???
software error genomicfeatures
updated 8.5 years ago by ★ 11k • written 8.5 years ago by • 0
1
vote
3
replies
1.5k
views
GenomicFeatures should support old 'Db type' value
genomicfeatures
8.5 years ago matt.chambers42 ▴ 10
2
votes
7
replies
1.8k
views
Peaks in coverageByTranscript {GenomicFeatures}
GenomicFeatures
updated 8.5 years ago by 16k • written 8.6 years ago by • 0
0
votes
1
reply
1.9k
views
Package dependency GenomicFeatures is installed but cannot be found
genomicfeatures bioclite package installation
8.6 years ago cqe20 • 0
0
votes
1
reply
1.6k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 8.6 years ago by 68k • written 8.6 years ago by • 0
1
vote
8
replies
2.9k
views
makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
GenomicFeatures
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 10
9
votes
3
replies
3.9k
views
Importing Gene Symbols with makeTxDbFromGFF
GenomicFeatures GFF3
updated 8.6 years ago by ★ 6.8k • written 8.6 years ago by ★ 1.6k
3
votes
2
replies
1.7k
views
Troubles with new version of GenomicFeatures(?)
software error R bioconductor genomicfeatures error message
8.6 years ago Walter F. Baumann ▴ 10
0
votes
1
reply
1.5k
views
warning in makeTxDbFromGFF
genomicfeatures
updated 8.6 years ago by 68k • written 8.6 years ago by • 0
8
votes
20
replies
7.4k
views
Issue when import genomic features from the file :Error in parseURI("") : cannot parse URI (issue resolved)
genomicfeatures xml libxml2
8.7 years ago JunLVI ▴ 40
5
votes
7
replies
2.5k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 40
1
vote
10
replies
4.4k
views
Issue creating a genomic state object in derfinder from an Ensembl GTF file
derfinder genomicfeatures
8.7 years ago Leonardo Collado Torres ★ 1.1k
0
votes
2
replies
1.1k
views
organism name error with makeTxDbPackageFromUCSC()
makeTxDbPackageFromUCSC genomicfeatures
8.7 years ago Ugo Borello ▴ 340
6
votes
6
replies
2.3k
views
GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
biomart maketxdbfrombiomart genomicfeatures
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 30
1
vote
2
replies
1.4k
views
Error while using GenomicFeatures package
genomicfeatures maketxdbfromgff
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 10
3
votes
13
replies
4.0k
views
Getting errors with makeTxDbFromBiomart
genomicfeatures biomart maketxdbfrombiomart
updated 8.8 years ago by ▴ 800 • written 8.8 years ago by ▴ 10
0
votes
1
reply
954
views
error in GenomicFeature
genomicfeatures
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
0
votes
1
reply
1.2k
views
count coverage for exact matches to sequence pattern
genomicfeatures rsamtools
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 80
2
votes
6
replies
2.0k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
2
votes
1
reply
1.5k
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 40
3
votes
5
replies
4.4k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno genomicfeatures
updated 9.0 years ago by ★ 4.3k • written 9.0 years ago by ▴ 370
3
votes
2
replies
2.7k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures gtf maketxdbfromgff iGenome
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 20
1
vote
23
replies
3.7k
views
Distance calculation for variants in intergenic regions
locatevariants variantannotation genomicfeatures
updated 9.0 years ago by ★ 11k • written 9.0 years ago by • 0
0
votes
1
reply
1.1k
views
warning message from makeTxDbFromGFF in GenomicFeatures package
genomicfeatures
updated 9.0 years ago by ★ 2.1k • written 9.0 years ago by ★ 4.3k
4
votes
3
replies
2.5k
views
How to extract only mRNA from TxDb object?
genomicfeatures
updated 3.3 years ago by ▴ 40 • written 9.0 years ago by ▴ 50
2
votes
2
replies
1.5k
views
Analysis of Ribo-seq with poly(A) mRNA RNA-seq
deseq2 genomicfeatures genomicalignments
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 50
1
vote
2
replies
1.6k
views
problems with GenomicFeatures::supportedUCSCtables("hg38")
genomicfeatures
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by ▴ 40
4
votes
2
replies
1.2k
views
How to extract transcripts from Txdb with length >100
genomicfeatures rtracklayer
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 50
2
votes
2
replies
3.3k
views
Get the genomic coordinates for the coding sequence (CDS) of a gene
genomicfeatures txdb.hsapiens.ucsc.hg19.knowngene cds
9.1 years ago madsheilskov ▴ 10
3
votes
5
replies
2.2k
views
Genomic features for genomic positions
genomicfeatures
updated 9.2 years ago by ▴ 160 • written 9.2 years ago by ▴ 290
1
vote
3
replies
1.5k
views
makeTxDbFromBiomart fails on Ensembl 85 human
biomart maketxdbfrombiomart genomicfeatures
9.2 years ago Ryan C. Thompson ★ 7.9k
6
votes
7
replies
3.1k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures maketxdbfromucsc refseq
updated 9.3 years ago by 16k • written 9.3 years ago by ▴ 10
1
vote
2
replies
3.1k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 9.3 years ago by 16k • written 9.3 years ago by ★ 4.1k
3
votes
5
replies
3.2k
views
makeTxDbFromGFF Error: subscript contains NAs or out-of-bounds indices - after package update
genomicfeatures
updated 9.4 years ago by 16k • written 9.4 years ago by • 0
5
votes
4
replies
2.0k
views
Is there a way to remove or take the first overlapping gene(s) when using makeTxDbFromGFF?
genomicfeatures
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 40
2
votes
4
replies
2.2k
views
supportedUCSCtables(genome="hg38"): Is ensGene track really available?
genomicfeatures
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 40
1
vote
2
replies
1.7k
views
mRNA start used instead of gene start in makeTxDbFromGFF
maketxdbfromgff genomicfeatures
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 80
291 results • Page 3 of 6
Recent ...
Replies
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)…
Votes
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
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
Popular Question to Hervé Pagès 16k
Popular Question to Ou, Jianhong ★ 1.3k
Popular Question to Maria Doyle ▴ 100
Locations • All
Barcelona, Spain, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
Germany, 1 hour ago
United States, 1 hour ago
Traffic: 1474 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