Showing : genomicfeatures • reset
9
votes
21
replies
14k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 10.1 years ago by ★ 1.3k • written 10.1 years ago by ▴ 200
9
votes
3
replies
4.2k
views
Importing Gene Symbols with makeTxDbFromGFF
GenomicFeatures GFF3
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by ★ 1.6k
8
votes
24
replies
5.3k
views
GenomicFeatures: Select exons by transcript. Any faster option than exonsBy?
GenomicFeatures
updated 9.9 years ago by 25k • written 9.9 years ago by ▴ 90
8
votes
6
replies
2.7k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 8.4 years ago by 16k • written 8.4 years ago by ▴ 20
8
votes
3
replies
7.0k
views
Renaming the seqlevels in a transcript database from GenomicFeatures
GenomicFeatures GenomicFeatures
updated 11.6 years ago by ▴ 390 • written 11.6 years ago by ▴ 320
8
votes
20
replies
7.7k
views
Issue when import genomic features from the file :Error in parseURI("") : cannot parse URI (issue resolved)
genomicfeatures xml libxml2
9.0 years ago • updated 8.9 years ago JunLVI ▴ 40
8
votes
12
replies
7.2k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 3.6 years ago by • 0 • written 10.9 years ago by ▴ 20
8
votes
16
replies
4.1k
views
Setting package name in makeTxDbPackage
genomicfeatures txdb
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ▴ 760
6
votes
6
replies
2.4k
views
GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
biomart maketxdbfrombiomart genomicfeatures
updated 9.0 years ago by 68k • written 9.0 years ago by ▴ 30
6
votes
7
replies
3.2k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures maketxdbfromucsc refseq
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 10
6
votes
14
replies
7.5k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 11.1 years ago by 53k • written 11.1 years ago by • 0
6
votes
5
replies
7.3k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 3.8 years ago by 16k • written 7.0 years ago by • 0
5
votes
3
replies
2.9k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
11.0 years ago • updated 10.8 years ago Thomas Girke ★ 1.7k
5
votes
5
replies
2.9k
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 5.0 years ago by ★ 1.6k • written 6.5 years ago by ▴ 10
5
votes
6
replies
4.5k
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 7.0 years ago by 16k • written 7.0 years ago by • 0
5
votes
4
replies
2.3k
views
GenomicFeatures and custom genomes?
genomicfeatures
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 10
5
votes
2
replies
3.9k
views
Saving/loading TxDb objects
genomicfeatures
updated 10.7 years ago by 25k • written 10.7 years ago by 68k
5
votes
4
replies
3.7k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 8.6 years ago by ★ 1.6k • written 8.6 years ago by ★ 3.4k
5
votes
2
replies
1.8k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.4 years ago Pratik Mehta ▴ 10
5
votes
9
replies
2.6k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.5 years ago by 43k • written 3.8 years ago by • 0
5
votes
4
replies
2.2k
views
Is there a way to remove or take the first overlapping gene(s) when using makeTxDbFromGFF?
genomicfeatures
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 40
5
votes
7
replies
2.6k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 40
5
votes
5
replies
3.0k
views
makeTxDbFromUCSC("hg19", "refGene") gives "not supported" error
genomicfeatures
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 20
4
votes
2
replies
2.1k
views
Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more genes than without restriction
GenomicFeatures
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 10
4
votes
5
replies
1.7k
views
Write multiple UTRs for a gene to a fasta file
genomicranges genomicfeatures
updated 10.0 years ago by ★ 11k • written 10.0 years ago by ▴ 90
4
votes
3
replies
2.6k
views
How to extract only mRNA from TxDb object?
genomicfeatures
updated 3.5 years ago by ▴ 40 • written 9.3 years ago by ▴ 50
4
votes
5
replies
4.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 2.0 years ago by ▴ 10 • written 10.2 years ago by ▴ 10
4
votes
2
replies
1.8k
views
Count reads with package "bamsignals" from a female bam file (no chrY)
bamsignals genomicfeatures
updated 10.7 years ago by ▴ 20 • written 10.7 years ago by ▴ 10
4
votes
7
replies
3.6k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart genomicfeatures txdb biomart
updated 10.3 years ago by 68k • written 10.3 years ago by ▴ 50
4
votes
3
replies
5.2k
views
subsetting GRanges object based on gene IDs
genomicranges genomicfeatures granges subsetting
8.4 years ago Assa Yeroslaviz ★ 1.5k
4
votes
9
replies
3.3k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 12 months ago by ★ 3.4k • written 13 months ago by ▴ 20
4
votes
3
replies
4.1k
views
TxDb error: external pointer is not valid
software error GenomicFeatures
6.4 years ago O. William McClung • 0
4
votes
2
replies
1.6k
views
Get internal exons using GenomicFeatures
genomicfeatures granges
updated 9.8 years ago by ★ 11k • written 9.8 years ago by ▴ 10
4
votes
2
replies
1.8k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by ▴ 80
4
votes
2
replies
1.3k
views
How to extract transcripts from Txdb with length >100
genomicfeatures rtracklayer
updated 9.4 years ago by 25k • written 9.4 years ago by ▴ 50
4
votes
8
replies
3.3k
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
2.9 years ago davidhillis • 0
3
votes
1
reply
3.9k
views
How does GenomicFeature calculate 3'UTR?
genomicfeatures annotation utr
updated 7.6 years ago by 16k • written 7.6 years ago by • 0
3
votes
5
replies
4.5k
views
Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno genomicfeatures
updated 9.2 years ago by ★ 4.3k • written 9.2 years ago by ▴ 370
3
votes
6
replies
2.7k
views
cummeRbund installation fails
bioconductor cummerbund software error GenomicFeatures
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 30
3
votes
2
replies
2.9k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures gtf maketxdbfromgff iGenome
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 20
3
votes
13
replies
4.2k
views
Getting errors with makeTxDbFromBiomart
genomicfeatures biomart maketxdbfrombiomart
updated 9.0 years ago by ▴ 800 • written 9.0 years ago by ▴ 10
3
votes
1
reply
1.1k
views
Error in makeTxDbFromBiomart for fungi_mart
genomicfeatures biomart
8.1 years ago JohnTownsend ▴ 20
3
votes
13
replies
3.8k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder genomicfeatures genomicranges
updated 8.5 years ago by ★ 1.1k • written 8.5 years ago by ▴ 20
3
votes
5
replies
2.3k
views
Genomic features for genomic positions
genomicfeatures
updated 9.5 years ago by ▴ 160 • written 9.5 years ago by ▴ 290
3
votes
2
replies
1.7k
views
gene model generation support?
granges gene models GenomicFeatures
10.8 years ago • updated 10.5 years ago Vincent J. Carey, Jr. 6.7k
3
votes
7
replies
2.7k
views
Add up RLEs that are in lists?
RLE GenomicFeatures rnaseq
updated 10.8 years ago by 16k • written 10.8 years ago by ▴ 30
3
votes
7
replies
3.6k
views
Failed to set session genome to ...
genomicfeatures makeTxDbFromUCSC
updated 10.3 years ago by ★ 11k • written 10.8 years ago by ▴ 100
3
votes
10
replies
6.1k
views
Getting a list of all tRNA encoding genes for an organism?
trna ncrna genomicfeatures featuredb biomart
updated 10.8 years ago by 16k • written 10.9 years ago by ▴ 180
3
votes
5
replies
3.3k
views
makeTxDbFromGFF Error: subscript contains NAs or out-of-bounds indices - after package update
genomicfeatures
updated 9.7 years ago by 16k • written 9.7 years ago by • 0
3
votes
2
replies
2.2k
views
Problem with TxDb.Mmusculus.UCSC.mm9.knownGene
software error txdb.mmusculus.ucsc.mm9.knowngene genomicfeatures
updated 11.0 years ago by 16k • written 11.0 years ago by • 0
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Answer: DiffBind differential analysis
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