Showing : genomicfeatures • reset
9
votes
21
replies
12k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 9.2 years ago by ★ 1.3k • written 9.2 years ago by ▴ 200
9
votes
3
replies
3.7k
views
Importing Gene Symbols with makeTxDbFromGFF
GenomicFeatures GFF3
updated 8.0 years ago by ★ 6.8k • written 8.0 years ago by ★ 1.6k
8
votes
24
replies
4.4k
views
GenomicFeatures: Select exons by transcript. Any faster option than exonsBy?
GenomicFeatures
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 90
8
votes
6
replies
2.3k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 7.6 years ago by 16k • written 7.6 years ago by ▴ 20
8
votes
3
replies
6.7k
views
Renaming the seqlevels in a transcript database from GenomicFeatures
GenomicFeatures GenomicFeatures
updated 10.8 years ago by ▴ 390 • written 10.8 years ago by ▴ 320
8
votes
20
replies
6.8k
views
Issue when import genomic features from the file :Error in parseURI("") : cannot parse URI (issue resolved)
genomicfeatures xml libxml2
8.1 years ago • updated 8.0 years ago JunLVI ▴ 40
8
votes
12
replies
6.4k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.7 years ago by • 0 • written 10.0 years ago by ▴ 20
8
votes
16
replies
3.3k
views
Setting package name in makeTxDbPackage
genomicfeatures txdb
updated 9.9 years ago by ★ 7.2k • written 9.9 years ago by ▴ 760
6
votes
6
replies
2.2k
views
GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
biomart maketxdbfrombiomart genomicfeatures
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 30
6
votes
7
replies
2.9k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures maketxdbfromucsc refseq
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 10
6
votes
14
replies
6.7k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 10.2 years ago by 52k • written 10.2 years ago by • 0
6
votes
5
replies
6.3k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 2.9 years ago by 16k • written 6.1 years ago by • 0
5
votes
3
replies
2.6k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
10.1 years ago • updated 10.0 years ago Thomas Girke ★ 1.7k
5
votes
5
replies
2.5k
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 4.1 years ago by ★ 1.6k • written 5.6 years ago by ▴ 10
5
votes
6
replies
4.1k
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 6.2 years ago by 16k • written 6.2 years ago by • 0
5
votes
4
replies
1.9k
views
GenomicFeatures and custom genomes?
genomicfeatures
updated 7.4 years ago by 16k • written 7.5 years ago by ▴ 10
5
votes
2
replies
3.6k
views
Saving/loading TxDb objects
genomicfeatures
updated 9.8 years ago by 25k • written 9.8 years ago by 68k
5
votes
4
replies
3.1k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ★ 3.4k
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
3.5 years ago Pratik Mehta ▴ 10
5
votes
9
replies
2.1k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 2.6 years ago by 43k • written 3.0 years ago by • 0
5
votes
4
replies
1.9k
views
Is there a way to remove or take the first overlapping gene(s) when using makeTxDbFromGFF?
genomicfeatures
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 40
5
votes
7
replies
2.3k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 40
5
votes
5
replies
2.7k
views
makeTxDbFromUCSC("hg19", "refGene") gives "not supported" error
genomicfeatures
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 20
4
votes
2
replies
1.9k
views
Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more genes than without restriction
GenomicFeatures
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 10
4
votes
5
replies
1.5k
views
Write multiple UTRs for a gene to a fasta file
genomicranges genomicfeatures
updated 9.1 years ago by ★ 11k • written 9.1 years ago by ▴ 90
4
votes
3
replies
2.3k
views
How to extract only mRNA from TxDb object?
genomicfeatures
updated 2.7 years ago by ▴ 40 • written 8.4 years ago by ▴ 50
4
votes
5
replies
3.8k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 14 months ago by ▴ 10 • written 9.3 years ago by ▴ 10
4
votes
2
replies
1.6k
views
Count reads with package "bamsignals" from a female bam file (no chrY)
bamsignals genomicfeatures
updated 9.8 years ago by ▴ 20 • written 9.8 years ago by ▴ 10
4
votes
7
replies
3.2k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart genomicfeatures txdb biomart
updated 9.4 years ago by 68k • written 9.4 years ago by ▴ 50
4
votes
3
replies
4.7k
views
subsetting GRanges object based on gene IDs
genomicranges genomicfeatures granges subsetting
7.6 years ago Assa Yeroslaviz ★ 1.5k
4
votes
9
replies
2.2k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 8 weeks ago by ★ 3.4k • written 3 months ago by ▴ 20
4
votes
3
replies
3.7k
views
TxDb error: external pointer is not valid
software error GenomicFeatures
5.5 years ago O. William McClung • 0
4
votes
2
replies
1.3k
views
Get internal exons using GenomicFeatures
genomicfeatures granges
updated 8.9 years ago by ★ 11k • written 8.9 years ago by ▴ 10
4
votes
2
replies
1.6k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by ▴ 80
4
votes
2
replies
1.1k
views
How to extract transcripts from Txdb with length >100
genomicfeatures rtracklayer
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 50
4
votes
8
replies
2.4k
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
2.0 years ago davidhillis • 0
3
votes
1
reply
3.2k
views
How does GenomicFeature calculate 3'UTR?
genomicfeatures annotation utr
updated 6.7 years ago by 16k • written 6.7 years ago by • 0
3
votes
5
replies
4.2k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno genomicfeatures
updated 8.4 years ago by ★ 4.3k • written 8.4 years ago by ▴ 370
3
votes
6
replies
2.2k
views
cummeRbund installation fails
bioconductor cummerbund software error GenomicFeatures
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 30
3
votes
2
replies
2.5k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures gtf maketxdbfromgff iGenome
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 20
3
votes
13
replies
3.7k
views
Getting errors with makeTxDbFromBiomart
genomicfeatures biomart maketxdbfrombiomart
updated 8.2 years ago by ▴ 800 • written 8.2 years ago by ▴ 10
3
votes
1
reply
948
views
Error in makeTxDbFromBiomart for fungi_mart
genomicfeatures biomart
7.2 years ago JohnTownsend ▴ 20
3
votes
13
replies
3.0k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder genomicfeatures genomicranges
updated 7.6 years ago by ★ 1.1k • written 7.6 years ago by ▴ 20
3
votes
5
replies
2.0k
views
Genomic features for genomic positions
genomicfeatures
updated 8.6 years ago by ▴ 160 • written 8.6 years ago by ▴ 290
3
votes
2
replies
1.4k
views
gene model generation support?
granges gene models GenomicFeatures
9.9 years ago • updated 9.6 years ago Vincent J. Carey, Jr. 6.7k
3
votes
7
replies
2.4k
views
Add up RLEs that are in lists?
RLE GenomicFeatures rnaseq
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 30
3
votes
7
replies
3.3k
views
Failed to set session genome to ...
genomicfeatures makeTxDbFromUCSC
updated 9.4 years ago by ★ 11k • written 9.9 years ago by ▴ 100
3
votes
10
replies
5.2k
views
Getting a list of all tRNA encoding genes for an organism?
trna ncrna genomicfeatures featuredb biomart
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 180
3
votes
5
replies
3.1k
views
makeTxDbFromGFF Error: subscript contains NAs or out-of-bounds indices - after package update
genomicfeatures
updated 8.8 years ago by 16k • written 8.8 years ago by • 0
3
votes
2
replies
2.0k
views
Problem with TxDb.Mmusculus.UCSC.mm9.knownGene
software error txdb.mmusculus.ucsc.mm9.knowngene genomicfeatures
updated 10.2 years ago by 16k • written 10.2 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Package developing and interoperation with Bioconductor by shepherl 4.1k
Using an example with SummarizedExperiment would satisfy the requirement; however the package should take the object directly and not just…
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Sofia • 0
1. I have tried to update the packages and R but to no avail. I keep getting either this error or : `Error in H5Fclose(file$H5Identifier) …
Comment: Validity of SingleR with very small bulk RNAseq reference by Rohit • 0
Hi @nhaus So, what did you end up doing in such a scenario? I am facing a similar challenge
Comment: CpGs with genomic positions greater than the chromosome size in EPICv2? by Joshua Llano • 0
Thank you for your reply James. I was worried that it was my mistake.
Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
Votes
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
Awards • All
Supporter to bhanu.chandra1 • 0
Popular Question to Gordon Smyth 52k
Popular Question to mdeea123 ▴ 10
Popular Question to GA ▴ 10
Popular Question to Elizabeth • 0
Locations • All
Australia, 4 minutes ago
The city by the bay, 13 minutes ago
WEHI, Melbourne, Australia, 28 minutes ago
United States, 32 minutes ago
United States, 1 hour ago
Traffic: 545 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