Showing : genomicfeatures • reset
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
8
votes
16
replies
3.3k
views
Setting package name in makeTxDbPackage
genomicfeatures txdb
updated 9.8 years ago by ★ 7.2k • written 9.9 years ago by ▴ 760
1
vote
7
replies
6.6k
views
Existence of a makeTxDbFromGFF function in GenomicFeatures package?
genomicfeatures
9.9 years ago pterry • 0
0
votes
8
replies
2.5k
views
makeTranscriptDbFromGFF Unexpected transcript duplicates
genomicfeatures
10.1 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
8
votes
20
replies
6.7k
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
2
votes
4
replies
2.1k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 40
5
votes
5
replies
2.7k
views
makeTxDbFromUCSC("hg19", "refGene") gives "not supported" error
genomicfeatures
updated 6.9 years ago by 68k • written 6.9 years ago by ▴ 20
0
votes
5
replies
4.2k
views
Fast way to find which gene a snp located.
SNP GenomicFeatures SNP GenomicFeatures
updated 13.9 years ago by ▴ 10 • written 13.9 years ago by ▴ 970
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
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
0
votes
4
replies
5.7k
views
Problem installing GenomicFeatures
GenomicFeatures GenomicFeatures
13.0 years ago Georg Otto ▴ 120
1
vote
8
replies
3.7k
views
GenomicFeatures package ERROR
software error genomicfeatures
updated 7.8 years ago by ★ 11k • written 9.3 years ago by • 0
2
votes
4
replies
5.2k
views
Gene Size using GenomicFeatures
genomicfeatures gene size gene length
updated 7.5 years ago by 16k • written 7.5 years ago by • 0
2
votes
3
replies
4.0k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 18 months ago by 52k • written 18 months ago by • 0
5
votes
4
replies
1.9k
views
GenomicFeatures and custom genomes?
genomicfeatures
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 10
0
votes
6
replies
3.7k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 9.7 years ago by 16k • written 9.7 years ago by ▴ 70
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
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
0
votes
6
replies
1.8k
views
[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt GenomicFeatures genomes Cancer Organism biomaRt GenomicFeatures
updated 13.0 years ago by ▴ 660 • written 13.0 years ago by 16k
0
votes
7
replies
2.2k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
updated 9.3 years ago by 16k • written 9.3 years ago by • 0
1
vote
3
replies
1.1k
views
Extract information from GenomicRanges
genomicranges genomicfeatures
9.0 years ago ribioinfo ▴ 100
1
vote
4
replies
1.9k
views
GenomicFeatures makeTranscriptDbFromBiomart 'chrominfo' data frame ... FAILED!
genomicfeatures
updated 9.2 years ago by 16k • written 9.2 years ago by ▴ 200
0
votes
2
replies
1.2k
views
GenomicFeatures coordinates UCSC
genomicfeatures txdb.hsapiens.ucsc.hg19.knowngene
8.9 years ago ribioinfo ▴ 100
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
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
0
votes
2
replies
1.2k
views
renamed seqlevels (TxDb) don't persist through a save-load cycle
GenomicFeatures TxDb
9.6 years ago • updated 9.5 years ago Robert K. Bradley ▴ 40
0
votes
7
replies
2.0k
views
Mapping genomic coordinates to transcript coordinates? (revived)
Biostrings GenomicFeatures Biostrings GenomicFeatures
updated 14.0 years ago by ★ 11k • written 14.1 years ago by 16k
0
votes
13
replies
3.3k
views
multiple hits with countOverlaps function
Sequencing GenomicFeatures Sequencing GenomicFeatures
13.9 years ago Wei Shi ★ 3.6k
0
votes
2
replies
1.3k
views
*Ranges paper published
Infrastructure IRanges GenomicFeatures GenomicRanges Infrastructure IRanges GenomicFeatures
updated 11.6 years ago by ★ 4.2k • written 11.6 years ago by ★ 11k
0
votes
3
replies
1.6k
views
possible conflict between renameSeqLevels (TxDb) and isActiveSeq (TxDb)
bug txdb genomicfeatures
9.6 years ago • updated 9.5 years ago Robert K. Bradley ▴ 40
0
votes
8
replies
5.5k
views
error making txdb object from gtf file
genomicfeatures
updated 9.2 years ago by ★ 2.1k • written 9.2 years ago by ▴ 20
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
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
7
replies
2.3k
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
4
replies
2.1k
views
Introns at transcript expression level
genomicfeatures iranges
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 20
1
vote
3
replies
1.4k
views
GenomicFeatures should support old 'Db type' value
genomicfeatures
7.9 years ago matt.chambers42 ▴ 10
2
votes
13
replies
2.9k
views
makeTranscriptDbFromBiomart failure from Data Anomaly
biomart genomicfeatures
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 80
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
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
2
votes
16
replies
4.7k
views
TxDb annotations for human chrM
GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene annotation
10.2 years ago • updated 10.1 years ago Robert Castelo ★ 3.4k
0
votes
7
replies
1.4k
views
GenomicFeatures::makeTranscriptDbFromGTF?
Cancer GenomicFeatures Cancer GenomicFeatures
updated 13.1 years ago by ★ 11k • written 13.1 years ago by ★ 13k
0
votes
4
replies
1.6k
views
Error in makeTranscriptDbFromGFF
deseq2 genomicfeatures
updated 10.0 years ago by 16k • written 10.0 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
0
votes
3
replies
1.2k
views
[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt GenomicFeatures Cancer Organism biomaRt GenomicFeatures
updated 13.1 years ago by ▴ 660 • written 13.1 years ago by ★ 1.6k
0
votes
2
replies
8.5k
views
Error with "library("GenomicFeatures")" - "there is no package called ‘XML’"
genomicfeatures xml loadnamespace
9.9 years ago greg.mulhearn • 0
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
0
votes
2
replies
2.6k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 10.8 years ago by ★ 7.2k • written 10.8 years ago by ★ 13k
2
votes
7
replies
5.5k
views
Extend GRanges start/end
Genetics GenomicFeatures Genetics GenomicFeatures
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ▴ 510
0
votes
4
replies
3.5k
views
How can I extract promoter regions from a list NCBI genbank acc?
GenomicFeatures GenomicFeatures
updated 12.4 years ago by ★ 7.2k • written 12.4 years ago by ▴ 200
1
vote
2
replies
1.5k
views
Missing values when extracting 5'UTR using GenomicFeatures?
GenomicFeatures 5'UTR
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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