Showing : genomicfeatures • reset
0
votes
5
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105
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
15 days ago • updated 14 days ago sieminsk • 0
2
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2
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116
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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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135
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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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96
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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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150
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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
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 8 weeks ago by ▴ 80 • written 6 months ago by • 0
0
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1
reply
264
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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217
views
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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177
views
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
79
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 10 months ago by 56k • written 10 months ago by ▴ 90
0
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2
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116
views
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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89
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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
votes
2
replies
84
views
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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272
views
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
replies
166
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
vote
2
replies
103
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 13 months ago by 13k • written 13 months ago by ▴ 40
0
votes
0
replies
107
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
votes
2
replies
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
replies
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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176
views
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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236
views
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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118
views
SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
17 months ago rmash • 0
4
votes
3
replies
649
views
TxDb error: external pointer is not valid
software error GenomicFeatures
18 months ago O. William McClung • 0
0
votes
2
replies
269
views
Error while creating txDb from gtf file
genomicfeatures
19 months ago bioinagesh • 0
3
votes
5
replies
303
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 7 weeks ago by ★ 1.5k • written 19 months ago by • 0
0
votes
1
reply
251
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
votes
0
replies
334
views
error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
24 months ago xvazquezc • 0
0
votes
0
replies
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
votes
3
replies
545
views
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
votes
6
replies
576
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 2.2 years ago by 14k • written 2.2 years ago by • 0
0
votes
5
replies
308
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
replies
482
views
makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
2.4 years ago DMA1 ▴ 10
0
votes
2
replies
400
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
2.5 years ago A ▴ 40
0
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1
reply
374
views
NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 2.5 years ago by 56k • written 2.5 years ago by • 0
0
votes
0
replies
411
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
2.6 years ago Wojeff • 0
1
vote
8
replies
868
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
votes
1
reply
696
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
votes
1
reply
515
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
votes
5
replies
459
views
Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
2.7 years ago michael.weber.1 • 0
0
votes
1
reply
478
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 2.7 years ago by ▴ 50 • written 2.8 years ago by • 0
1
vote
1
reply
359
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
622
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
764
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
544
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
2.9 years ago Ina Hoeschele ▴ 610
0
votes
2
replies
499
views
Cannot get TxDb object using makeTxDbFromUCSC in any table:
software error genomicfeatures
updated 2.9 years ago by 56k • written 2.9 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
Recent ...
Replies
Answer: DepMap copy number by Laurent Gatto 1.5k
Hi Danny - sorry for the delay in answering, I hadn't set `depmap` as a tag yet. Yes, that bug has been fixed in the devel version.
Answer: High fold change reported for comparison of samples with zero values in all samp by James W. MacDonald 56k
The universal recommendation is to remove all genes with consistently low (or all zero) expression values prior to doing any modeling. It i…
Comment: Sample quality weights for RNA-seq by Naomi Altman ★ 6.0k
Thanks Michael. I'll try that. (Limma folks, I'd still love to hear from you.)
Answer: Installation error if message implemented in .Rprofile by Mike Smith ★ 4.9k
A similar issue has been reported recently for rhdf5filters (https://github.com/grimbough/rhdf5filters/issues/11) and rhdf5 (https://github…
Comment: Couldn't load org.Hs.eg.db by Xulei Huo • 0
That does not work, i have tried it.
Votes
Answer: TargetsFile. Where it is?
Answer: TargetsFile. Where it is?
Comment: TargetsFile. Where it is?
Comment: Using DESeq2 to identify changing transcriptional activity in a metagenome
Answer: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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