Showing : genomicfeatures • reset
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
9 days ago António Miguel de Jesus Domingues ▴ 480
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5
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135
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
5 weeks ago sieminsk • 0
2
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2
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144
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makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
10 weeks ago erhoppe • 0
0
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6
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156
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Splitting TxDb by Strand
GenomicFeatures TxDb
3 months ago rproendo • 0
0
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2
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108
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Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
6 months ago • updated 5 months ago k.vitting.seerup ▴ 100
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2
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169
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Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 6 months ago by 32k • written 6 months ago by • 0
0
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1
reply
118
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 12 weeks ago by ▴ 80 • written 6 months ago by ▴ 10
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1
reply
309
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Add gene symbol when making TxDb
txdb genomicfeatures
updated 8 months ago by 56k • written 8 months ago by ▴ 70
3
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7
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233
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GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 9 months ago by 56k • written 9 months ago by ▴ 10
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1
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132
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error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 9 months ago by 2.6k • written 9 months ago by • 0
3
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6
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200
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TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 9 months ago by 25k • written 9 months ago by ▴ 120
0
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1
reply
88
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makeTxDbFromGFF warning meaning
GenomicFeatures
updated 11 months ago by 56k • written 11 months ago by ▴ 90
0
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2
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125
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How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 11 months ago by 11k • written 11 months ago by ▴ 10
0
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0
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102
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
12 months ago shangguandong1996 ▴ 20
0
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2
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93
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 12 months ago by 56k • written 12 months ago by ▴ 30
2
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3
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289
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Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 13 months ago by 56k • written 13 months ago by ▴ 60
3
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4
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188
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how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 13 months ago by 14k • written 13 months ago by ▴ 20
1
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2
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112
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 14 months ago by 13k • written 14 months ago by ▴ 40
0
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0
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116
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 14 months ago by 2.6k • written 14 months ago by • 0
0
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2
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94
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biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 15 months ago by 56k • written 15 months ago by • 0
6
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11
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2.8k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 15 months ago by • 0 • written 6.1 years ago by ▴ 20
2
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3
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122
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 15 months ago by 56k • written 15 months ago by ▴ 10
0
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3
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188
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Resize exons in transcript to total width
genomicranges genomicfeatures
updated 16 months ago by 11k • written 16 months ago by ▴ 70
0
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8
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251
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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 18 months ago by 14k • written 18 months ago by ▴ 70
0
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0
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125
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
18 months ago rmash • 0
4
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3
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687
views
TxDb error: external pointer is not valid
software error GenomicFeatures
19 months ago O. William McClung • 0
0
votes
2
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280
views
Error while creating txDb from gtf file
genomicfeatures
20 months ago bioinagesh • 0
3
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5
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338
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threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 10 weeks ago by ★ 1.5k • written 20 months ago by • 0
0
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1
reply
263
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 2.0 years ago by 14k • written 2.0 years ago by ▴ 10
0
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0
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358
views
error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
2.1 years ago xvazquezc • 0
0
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0
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215
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Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 2.1 years ago by 25k • written 2.1 years ago by • 0
4
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3
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597
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Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 2.2 years ago by 14k • written 2.2 years ago by • 0
5
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6
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596
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 2.3 years ago by 14k • written 2.3 years ago by • 0
0
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5
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323
views
GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 2.4 years ago by 56k • written 2.4 years ago by ★ 1.5k
1
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2
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496
views
makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
2.5 years ago DMA1 ▴ 10
0
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2
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413
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
2.6 years ago A ▴ 40
0
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1
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383
views
NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 2.6 years ago by 56k • written 2.6 years ago by • 0
0
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0
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428
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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
2.6 years ago Wojeff • 0
1
vote
8
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883
views
Trying to map nucleotide position from a transcript to genomic location
genomicfeatures mapfromtranscripts mirna
updated 2.6 years ago by ★ 6.7k • written 2.6 years ago by ▴ 20
0
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1
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709
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
2.7 years ago jerrywu1987 • 0
1
vote
1
reply
437
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 2.8 years ago by ▴ 20 • written 2.8 years ago by • 0
0
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1
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533
views
getting mouse gene ids from makeTxDbFromUCSC()
GenomicFeatures makeTxDbFromUCSC
updated 2.8 years ago by 2.6k • written 2.8 years ago by • 0
0
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5
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479
views
Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
2.8 years ago michael.weber.1 • 0
0
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1
reply
500
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 2.8 years ago by ▴ 50 • written 2.8 years ago by • 0
1
vote
1
reply
372
views
makeTxdbFromUCSC fails to download
maketxdbpackagefromucsc rtracklayer genomicfeatures
updated 2.8 years ago by 56k • written 2.8 years ago by • 0
0
votes
1
reply
1.2k
views
TxDb.Hsapiens.UCSC.hg19.knownGen installation fail - non-zero exit status
software error package installation genomicfeatures
updated 2.8 years ago by 25k • written 2.8 years ago by • 0
3
votes
1
reply
655
views
How does GenomicFeature calculate 3'UTR?
genomicfeatures annotation utr
updated 2.8 years ago by 14k • written 2.9 years ago by • 0
1
vote
3
replies
782
views
GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
genomicfeatures
updated 2.9 years ago by 56k • written 2.9 years ago by ▴ 30
0
votes
1
reply
562
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
2.9 years ago Ina Hoeschele ▴ 610
0
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2
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508
views
Cannot get TxDb object using makeTxDbFromUCSC in any table:
software error genomicfeatures
updated 3.0 years ago by 56k • written 3.0 years ago by • 0
262 results • Page 1 of 6
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Comment: Limma paired analysis design question by jefflincoln4 • 0
Thank you Gordon. One more thing, why use the log of blood iron concentration?
Answer: Limma paired analysis design question by Gordon Smyth 42k
Just put (log) blood iron concentration and `pair` in the design matrix. limma will work with differences automatically -- there's no need…
Comment: Extracting the findPalindrome() results by Hervé Pagès 14k
Also, you have a point: the output of `Biostrings::findPalindromes()` is an XStringViews object and `as.data.frame()` does a poor job on th…
Comment: Compute fgsea with my own database with R version 4.0.2 by assaron ▴ 190
I'm not sure what would be the best course of action in your case, if there is one at all, but I'd suggest to keep the ranking on the gene-…
Comment: Error installing Deseq2 by ATpoint ▴ 590
Go through the error logs and find the first error, this is where you have to start debugging, this here is just the consequences of the in…
Votes
Comment: DESeq2 with high range of within-group variability
Comment: problem regarding differential gene express analysis
Comment: Normalisation in DESeq2
Answer: Compute fgsea with my own database with R version 4.0.2
Comment: lmFit, number of proteins
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