Showing : genomicfeatures • reset
5
votes
4
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2.2k
views
GenomicFeatures and custom genomes?
genomicfeatures
updated 8.1 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 8.2 years ago by 16k • written 8.2 years ago by • 0
2
votes
2
replies
5.5k
views
Could not find function "makeTranscriptDbFromGFF"
GenomicFeatures makeTranscriptDbFromGFF gff annotation
updated 8.2 years ago by ★ 11k • written 8.2 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 8.4 years ago by • 0
3
votes
13
replies
3.6k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder genomicfeatures genomicranges
updated 8.3 years ago by ★ 1.1k • written 8.3 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
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1.8k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 8.4 years ago by 43k • written 8.4 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 8.4 years ago by ★ 1.6k • written 8.4 years ago by ★ 3.4k
0
votes
1
reply
795
views
Issues with .extractEnsemblReleaseFromDbVersion() and get_organism_from_Ensembl_Mart_dataset()
genomicfeatures
updated 8.5 years ago by 16k • written 8.5 years ago by ▴ 10
1
vote
8
replies
4.1k
views
GenomicFeatures package ERROR
software error genomicfeatures
updated 8.5 years ago by ★ 11k • written 10.0 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
1.6k
views
GenomicFeatures should support old 'Db type' value
genomicfeatures
8.6 years ago matt.chambers42 ▴ 10
2
votes
7
replies
1.8k
views
Peaks in coverageByTranscript {GenomicFeatures}
GenomicFeatures
updated 8.6 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 8.7 years ago by 16k • written 8.7 years ago by ▴ 10
9
votes
3
replies
4.0k
views
Importing Gene Symbols with makeTxDbFromGFF
GenomicFeatures GFF3
updated 8.7 years ago by ★ 6.8k • written 8.7 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
8.7 years ago Walter F. Baumann ▴ 10
0
votes
1
reply
1.5k
views
warning in makeTxDbFromGFF
genomicfeatures
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
8
votes
20
replies
7.5k
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
2.6k
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
8.8 years ago Ugo Borello ▴ 340
6
votes
6
replies
2.3k
views
GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
biomart maketxdbfrombiomart genomicfeatures
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 30
1
vote
2
replies
1.4k
views
Error while using GenomicFeatures package
genomicfeatures maketxdbfromgff
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 10
3
votes
13
replies
4.1k
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
970
views
error in GenomicFeature
genomicfeatures
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
0
votes
1
reply
1.2k
views
count coverage for exact matches to sequence pattern
genomicfeatures rsamtools
updated 8.9 years ago by ★ 11k • written 8.9 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 9.0 years ago by 43k • written 9.0 years ago by • 0
2
votes
1
reply
1.5k
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 9.0 years ago by 68k • written 9.0 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
2.8k
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
3.8k
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 9.1 years ago by ▴ 50
2
votes
2
replies
1.6k
views
Analysis of Ribo-seq with poly(A) mRNA RNA-seq
deseq2 genomicfeatures genomicalignments
updated 9.1 years ago by 43k • written 9.1 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 9.2 years ago by ▴ 40
4
votes
2
replies
1.3k
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
9.2 years ago madsheilskov ▴ 10
3
votes
5
replies
2.2k
views
Genomic features for genomic positions
genomicfeatures
updated 9.3 years ago by ▴ 160 • written 9.3 years ago by ▴ 290
1
vote
3
replies
1.5k
views
makeTxDbFromBiomart fails on Ensembl 85 human
biomart maketxdbfrombiomart genomicfeatures
9.3 years ago Ryan C. Thompson ★ 7.9k
6
votes
7
replies
3.2k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures maketxdbfromucsc refseq
updated 9.4 years ago by 16k • written 9.4 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 9.4 years ago by 16k • written 9.4 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 9.5 years ago by 16k • written 9.5 years ago by • 0
5
votes
4
replies
2.1k
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
2.3k
views
supportedUCSCtables(genome="hg38"): Is ensGene track really available?
genomicfeatures
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 40
1
vote
2
replies
1.7k
views
mRNA start used instead of gene start in makeTxDbFromGFF
maketxdbfromgff genomicfeatures
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 80
291 results • Page 3 of 6
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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