Showing : GenomicFeatures • reset
1
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144
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GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 29 days ago by 58k • written 29 days ago by ▴ 20
1
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2
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224
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
9 weeks ago • updated 8 weeks ago Madza Farias-Virgens • 0
2
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3
replies
195
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How to get longest isoform
GenomicFeatures Biostrings
updated 9 weeks ago by 15k • written 9 weeks ago by • 0
1
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2
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170
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NAs in my txdb tx_name
GenomicFeatures Biostrings
9 weeks ago Madza Farias-Virgens • 0
2
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2
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168
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Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 9 weeks ago by 15k • written 10 weeks ago by • 0
5
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2
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289
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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192
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install GenomicFeatures fail
GenomicFeatures install
updated 5 months ago by 58k • written 5 months ago by ▴ 80
1
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4
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244
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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230
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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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135
views
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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177
views
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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528
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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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461
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makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
11 months ago erhoppe • 0
0
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6
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388
views
Splitting TxDb by Strand
GenomicFeatures TxDb
11 months ago rproendo ▴ 20
0
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3
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277
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Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 11 weeks ago by • 0 • written 14 months ago by ▴ 100
0
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2
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648
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
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1
reply
247
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
845
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 17 months ago by 58k • written 17 months ago by ▴ 90
3
votes
7
replies
549
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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336
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 18 months ago by 2.9k • written 18 months ago by • 0
3
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6
replies
449
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
210
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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272
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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272
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
21 months ago Guandong Shang ▴ 20
0
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2
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198
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 21 months ago by 58k • written 21 months ago by ▴ 30
2
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3
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600
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 22 months ago by 58k • written 22 months ago by ▴ 80
3
votes
4
replies
417
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
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304
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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264
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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316
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 24 months ago by 58k • written 24 months ago by • 0
6
votes
11
replies
3.3k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 24 months ago by • 0 • written 6.8 years ago by ▴ 20
2
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3
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264
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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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364
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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482
views
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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262
views
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
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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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599
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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405
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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601
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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323
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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1.2k
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
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848
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
replies
471
views
GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 3.2 years ago by 58k • written 3.2 years ago by ★ 1.5k
1
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2
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630
views
makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
3.2 years ago DMA1 ▴ 10
0
votes
2
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550
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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506
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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699
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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 3.4 years ago by ▴ 20
0
votes
1
reply
934
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: Need help for ProStaR Stand-alone install by benoit.marchand • 0
Thank you for answering. I've just updated to Prostar v1.26.3 and confirm that the **Prostar()** command **now works** in R for me on linu…
Answer: airway package not compatible with R version 4.1.2 (2021-11-01) by ATpoint ▴ 970
`data(airway)` is your friend. The CRAN error comes from the fact that it is not a CRAN package, not that it is a version problem itself.
Comment: airway package not compatible with R version 4.1.2 (2021-11-01) by Lluís Revilla Sancho ▴ 660
I think it would help if you try again to install it via `BiocManager::install("airway")` and report the exact text output (without quittin…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by Michael Love 35k
This looks as expected with the control genes centered on the x-axis (yes, these can have high variance, this is discussed in work by Risso…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by argonvibio • 0
Hello Michael, and thank you for your reply. I have done as you described, estimating size factors with controlGenes before DESeq, but the…
Votes
Comment: Need help for ProStaR Stand-alone install
Emirical Bayesian shrinkage for dispertion/LFC estimation
C: Emirical Bayesian shrinkage for dispertion/LFC estimation
A: Emirical Bayesian shrinkage for dispertion/LFC estimation
Comment: airway package not compatible with R version 4.1.2 (2021-11-01)
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