Showing : GenomicFeatures • reset
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2 hours ago Matthias Munz ▴ 10
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79
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3 months ago António Miguel de Jesus Domingues ▴ 480
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5
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262
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3 months ago sieminsk • 0
2
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2
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268
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makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
5 months ago erhoppe • 0
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6
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217
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Splitting TxDb by Strand
GenomicFeatures TxDb
5 months ago rproendo • 0
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2
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155
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Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
8 months ago k.vitting.seerup ▴ 100
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2
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239
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Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 8 months ago by 33k • written 8 months ago by • 0
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1
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169
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 5 months ago by ▴ 80 • written 9 months ago by ▴ 10
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1
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425
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Add gene symbol when making TxDb
txdb genomicfeatures
updated 11 months ago by 57k • written 11 months ago by ▴ 90
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7
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314
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GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 11 months ago by 57k • written 11 months ago by ▴ 10
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182
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error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 12 months ago by 2.8k • written 12 months ago by • 0
3
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6
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283
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TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 12 months ago by 25k • written 12 months ago by ▴ 120
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1
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122
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makeTxDbFromGFF warning meaning
GenomicFeatures
updated 14 months ago by 57k • written 14 months ago by ▴ 90
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2
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168
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How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 14 months ago by 11k • written 14 months ago by ▴ 10
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152
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
15 months ago Guandong Shang ▴ 20
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2
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127
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Error with makeTxDbFromBiomart
GenomicFeatures
updated 15 months ago by 57k • written 15 months ago by ▴ 30
2
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3
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379
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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 16 months ago by 57k • written 16 months ago by ▴ 60
3
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4
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266
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how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 16 months ago by 15k • written 16 months ago by ▴ 20
1
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2
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196
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Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 17 months ago by 13k • written 17 months ago by ▴ 40
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154
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Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 17 months ago by 2.8k • written 17 months ago by • 0
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2
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140
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biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 18 months ago by 57k • written 18 months ago by • 0
6
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11
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3.0k
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Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 18 months ago by • 0 • written 6.3 years ago by ▴ 20
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3
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168
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 18 months ago by 57k • written 18 months ago by ▴ 10
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3
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258
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Resize exons in transcript to total width
genomicranges genomicfeatures
updated 19 months ago by 11k • written 19 months ago by ▴ 90
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8
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334
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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 20 months ago by 15k • written 20 months ago by ▴ 70
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164
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
20 months ago rmash • 0
4
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3
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836
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TxDb error: external pointer is not valid
software error GenomicFeatures
22 months ago O. William McClung • 0
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2
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344
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Error while creating txDb from gtf file
genomicfeatures
23 months ago bioinagesh • 0
3
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5
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453
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threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 5 months ago by ★ 1.5k • written 23 months ago by • 0
0
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1
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303
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create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 2.2 years ago by 15k • written 2.2 years ago by ▴ 10
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0
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422
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error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
2.3 years ago xvazquezc • 0
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251
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Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 2.4 years ago by 25k • written 2.4 years ago by • 0
4
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3
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802
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Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 2.4 years ago by 15k • written 2.4 years ago by • 0
5
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6
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673
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error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 2.5 years ago by 15k • written 2.5 years ago by • 0
0
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5
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368
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GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 2.7 years ago by 57k • written 2.7 years ago by ★ 1.5k
1
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2
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539
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makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
2.7 years ago DMA1 ▴ 10
0
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2
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462
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Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
2.8 years ago A ▴ 40
0
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1
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419
views
NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 2.8 years ago by 57k • written 2.8 years ago by • 0
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0
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478
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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
2.8 years ago Wojeff • 0
1
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8
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1.0k
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Trying to map nucleotide position from a transcript to genomic location
genomicfeatures mapfromtranscripts mirna
updated 2.9 years ago by ★ 6.7k • written 2.9 years ago by ▴ 20
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1
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770
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getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
2.9 years ago jerrywu1987 • 0
1
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1
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505
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 3.0 years ago by ▴ 20 • written 3.0 years ago by • 0
0
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1
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578
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getting mouse gene ids from makeTxDbFromUCSC()
GenomicFeatures makeTxDbFromUCSC
updated 3.0 years ago by 2.8k • written 3.0 years ago by • 0
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5
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526
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Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
3.0 years ago michael.weber.1 • 0
0
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1
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547
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makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 3.0 years ago by ▴ 50 • written 3.0 years ago by • 0
1
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1
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403
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makeTxdbFromUCSC fails to download
maketxdbpackagefromucsc rtracklayer genomicfeatures
updated 3.0 years ago by 57k • written 3.0 years ago by • 0
0
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1
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1.3k
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TxDb.Hsapiens.UCSC.hg19.knownGen installation fail - non-zero exit status
software error package installation genomicfeatures
updated 3.0 years ago by 25k • written 3.0 years ago by • 0
3
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1
reply
746
views
How does GenomicFeature calculate 3'UTR?
genomicfeatures annotation utr
updated 3.1 years ago by 15k • written 3.1 years ago by • 0
1
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3
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838
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GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
genomicfeatures
updated 3.1 years ago by 57k • written 3.1 years ago by ▴ 30
0
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1
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619
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
3.2 years ago Ina Hoeschele ▴ 610
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Comment: cannot install edgeR on M1 Mac by noname88 • 0
Hi--I recommend seeing the suggestions in response to this post. It solved ALL of my problems with this type of installation! https://sta…
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Unfortunately, I have to save my time to address software related questions. For questions about how to set up your statistical analysis, I…
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*"I would like to compare the different "cell types" against each other while taking into account the "patient" and the "disease" effect."*…
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Answer: problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignmen
Answer: cannot install edgeR on M1 Mac
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