Showing : GenomicFeatures • reset
0
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5
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114
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
19 days ago • updated 18 days ago sieminsk • 0
2
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2
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123
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makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
7 weeks ago erhoppe • 0
0
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6
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138
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Splitting TxDb by Strand
GenomicFeatures TxDb
10 weeks ago rproendo • 0
0
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2
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97
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Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
5 months ago k.vitting.seerup ▴ 100
0
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2
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152
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Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5 months ago by 32k • written 5 months ago by • 0
0
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1
reply
107
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 9 weeks ago by ▴ 80 • written 6 months ago by • 0
0
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1
reply
273
views
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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220
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GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 8 months ago by 56k • written 8 months ago by ▴ 10
0
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1
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124
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 8 months ago by 2.6k • written 8 months ago by • 0
3
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6
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179
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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
80
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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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118
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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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91
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
11 months ago shangguandong1996 ▴ 20
0
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2
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85
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Error with makeTxDbFromBiomart
GenomicFeatures
updated 11 months ago by 56k • written 11 months ago by ▴ 30
2
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3
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274
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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 12 months ago by 56k • written 12 months ago by ▴ 60
3
votes
4
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167
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 12 months ago by 14k • written 13 months ago by ▴ 20
1
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2
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105
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 13 months ago by 13k • written 13 months ago by ▴ 40
0
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0
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108
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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89
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 14 months ago by 56k • written 14 months ago by • 0
6
votes
11
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2.8k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 14 months ago by • 0 • written 6.1 years ago by ▴ 20
2
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3
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112
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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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178
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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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237
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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 17 months ago by 14k • written 17 months ago by ▴ 70
0
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0
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119
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
17 months ago rmash • 0
4
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3
replies
653
views
TxDb error: external pointer is not valid
software error GenomicFeatures
19 months ago • updated 18 months ago O. William McClung • 0
0
votes
2
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269
views
Error while creating txDb from gtf file
genomicfeatures
20 months ago bioinagesh • 0
3
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5
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309
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 8 weeks ago by ★ 1.5k • written 20 months ago by • 0
0
votes
1
reply
254
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 23 months ago by 14k • written 23 months ago by ▴ 10
0
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0
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335
views
error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
2.0 years ago xvazquezc • 0
0
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0
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205
views
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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554
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Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 2.1 years ago by 14k • written 2.2 years ago by • 0
5
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6
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577
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error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 2.2 years ago by 14k • written 2.2 years ago by • 0
0
votes
5
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310
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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483
views
makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
2.4 years ago DMA1 ▴ 10
0
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2
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400
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
2.5 years ago A ▴ 40
0
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1
reply
375
views
NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 2.5 years ago by 56k • written 2.5 years ago by • 0
0
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0
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413
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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
replies
871
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
reply
698
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
2.6 years ago jerrywu1987 • 0
1
vote
1
reply
428
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 2.7 years ago by ▴ 20 • written 2.7 years ago by • 0
0
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1
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517
views
getting mouse gene ids from makeTxDbFromUCSC()
GenomicFeatures makeTxDbFromUCSC
updated 2.7 years ago by 2.6k • written 2.7 years ago by • 0
0
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5
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462
views
Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
2.7 years ago michael.weber.1 • 0
0
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1
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482
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
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1
reply
360
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
627
views
How does GenomicFeature calculate 3'UTR?
genomicfeatures annotation utr
updated 2.8 years ago by 14k • written 2.8 years ago by • 0
1
vote
3
replies
766
views
GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
genomicfeatures
updated 2.8 years ago by 56k • written 2.8 years ago by ▴ 30
0
votes
1
reply
545
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
2.9 years ago Ina Hoeschele ▴ 610
0
votes
2
replies
500
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
1
vote
1
reply
621
views
installation of "GenomicFeatures"
GenomicFeatures
updated 3.0 years ago by 56k • written 3.0 years ago by • 0
261 results • Page 1 of 6
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Answer: unable to forge custom BSgenome after update by Hervé Pagès 14k
Hi, You need to specify the `circ_seqs` field in your seed file. `forgeBSgenomeDataPkg()` needs to know which sequences are circular …
Comment: How to apply limma-trend or voom to batch corrected single cell data? (non-integ by hainct • 0
Thank you @alun
Comment: EnhancedVolcano plot with colCustom by Neeraja Vegesna ▴ 10
Hi Kevin, It worked once I added `names(keyvals.colour1)[keyvals.colour1 == '#8F8F8F'] <- 'NA'`. ![volcanoplot][1] Thanks a lot for you…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mwong043 • 0
Thanks Rory. I tried the first method by defining a vector containing the normalisation factors for my samples and it worked. I am just wo…
Comment: EnhancedVolcano plot with colCustom by Kevin Blighe 2.8k
Hi, that's great that it works with a lower number of groups. Can you re-check the logic flow when you are using more groups? *EnhancedVolc…
Votes
mgcv not updating
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Comment: EnhancedVolcano plot with colCustom
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