Showing : genomicfeatures • reset
1
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137
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GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 24 days ago by 58k • written 24 days ago by ▴ 20
1
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2
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213
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
8 weeks ago Madza Farias-Virgens • 0
2
votes
3
replies
192
views
How to get longest isoform
GenomicFeatures Biostrings
updated 8 weeks ago by 15k • written 8 weeks ago by • 0
1
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2
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169
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
8 weeks ago Madza Farias-Virgens • 0
2
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2
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167
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Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 9 weeks ago by 15k • written 9 weeks ago by • 0
5
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2
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285
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4 months ago Pratik Mehta ▴ 10
0
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1
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188
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install GenomicFeatures fail
GenomicFeatures install
updated 4 months ago by 58k • written 4 months ago by ▴ 80
1
vote
4
replies
241
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
5 months ago A.J. ▴ 20
1
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3
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228
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
5 months ago A.J. ▴ 20
0
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0
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133
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
5 months ago Matthias Munz ▴ 10
0
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0
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174
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
8 months ago António Miguel de Jesus Domingues ▴ 480
0
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5
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519
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
9 months ago sieminsk • 0
2
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2
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458
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makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
10 months ago erhoppe • 0
0
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6
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382
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Splitting TxDb by Strand
GenomicFeatures TxDb
11 months ago rproendo ▴ 20
0
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3
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272
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 10 weeks ago by • 0 • written 14 months ago by ▴ 100
0
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2
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631
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 14 months ago by 35k • written 14 months ago by • 0
0
votes
1
reply
246
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 11 months ago by ▴ 80 • written 15 months ago by ▴ 10
0
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1
reply
822
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 17 months ago by 58k • written 17 months ago by ▴ 90
3
votes
7
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534
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 17 months ago by 58k • written 17 months ago by ▴ 10
0
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1
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333
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 17 months ago by 2.9k • written 17 months ago by • 0
3
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6
replies
442
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 18 months ago by 25k • written 18 months ago by ▴ 120
0
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1
reply
209
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 20 months ago by 58k • written 20 months ago by ▴ 100
0
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2
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270
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 20 months ago by 11k • written 20 months ago by ▴ 10
0
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0
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269
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
20 months ago Guandong Shang ▴ 20
0
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2
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196
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 20 months ago by 58k • written 20 months ago by ▴ 30
2
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3
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594
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 21 months ago by 58k • written 21 months ago by ▴ 80
3
votes
4
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415
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 22 months ago by 15k • written 22 months ago by ▴ 20
1
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2
replies
303
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 22 months ago by 13k • written 22 months ago by ▴ 40
0
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0
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263
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 23 months ago by 2.9k • written 23 months ago by • 0
0
votes
2
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314
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 23 months ago by 58k • written 23 months ago by • 0
6
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11
replies
3.2k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 23 months ago by • 0 • written 6.8 years ago by ▴ 20
2
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3
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260
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 2.0 years ago by 58k • written 2.0 years ago by ▴ 10
0
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3
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360
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 2.1 years ago by 11k • written 2.1 years ago by ▴ 90
0
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8
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478
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exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 2.2 years ago by 15k • written 2.2 years ago by ▴ 70
0
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0
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260
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
2.2 years ago rmash • 0
4
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3
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1.2k
views
TxDb error: external pointer is not valid
software error GenomicFeatures
2.3 years ago O. William McClung • 0
0
votes
2
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461
views
Error while creating txDb from gtf file
genomicfeatures
2.4 years ago bioinagesh • 0
3
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5
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595
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 11 months ago by ★ 1.5k • written 2.4 years ago by • 0
0
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1
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403
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 2.7 years ago by 15k • written 2.7 years ago by ▴ 10
0
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0
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592
views
error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
2.8 years ago xvazquezc • 0
0
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0
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322
views
Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 2.8 years ago by 25k • written 2.8 years ago by • 0
4
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3
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1.1k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 2.9 years ago by 15k • written 2.9 years ago by • 0
5
votes
6
replies
841
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 3.0 years ago by 15k • written 3.0 years ago by • 0
0
votes
5
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468
views
GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 3.1 years ago by 58k • written 3.1 years ago by ★ 1.5k
1
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2
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628
views
makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
3.2 years ago DMA1 ▴ 10
0
votes
2
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549
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
3.3 years ago A ▴ 40
0
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1
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505
views
NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 3.3 years ago by 58k • written 3.3 years ago by • 0
0
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0
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687
views
GenomicFeatures: How to extract a gene's upstream region of TSS up to the end position of the flanking (nearby) gene.
genomicranges genomicfeatures promoter upstream_flank
3.3 years ago Wojeff • 0
1
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8
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1.2k
views
Trying to map nucleotide position from a transcript to genomic location
genomicfeatures mapfromtranscripts mirna
updated 3.3 years ago by ★ 6.7k • written 3.3 years ago by ▴ 20
0
votes
1
reply
931
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
3.4 years ago jerrywu1987 • 0
50 results • Page 1 of 1
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Comment: Cannot install Phyloseq and dada2 by Guido Hooiveld ★ 3.2k
Did you notice this message:? Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.0.0/libra…
Comment: Use of shrunken LFCs to address questions about the distribution of LFCs between by i.sudbery ▴ 20
Thanks Mike. I might have a play with stratifying by expression level. One reason I wasn't looking at gene set testing is that its the nul…
Answer: submitting a BSgenome package by deisianyufg • 0
From my Github repository. I am sorry, I thought the package was already released and realize now that is still only in my github reposito…
Comment: PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp by swbarnes2 ▴ 970
Is the one plot a mirror image of the other?
Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between by Michael Love 35k
hi Ian, Great question, and good to be concerned that the mean expression may be a confounder for either analysis, Why not stratify your…
Votes
Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between
Answer: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
Comment: submitting a BSgenome package
Answer: rlog vs vst for outlier identification
Answer: DESeq2 median of ratios normalization for signature score calculation
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