Showing : genomicfeatures • reset
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2 days 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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264
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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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270
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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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222
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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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240
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Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 9 months ago by 33k • written 9 months ago by • 0
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1
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170
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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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432
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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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316
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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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1
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184
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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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285
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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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125
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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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171
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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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153
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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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387
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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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272
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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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203
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 17 months ago by 13k • written 17 months ago by ▴ 40
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158
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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 6.4 years ago by ▴ 20
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3
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172
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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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260
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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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336
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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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166
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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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841
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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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346
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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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424
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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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816
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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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678
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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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376
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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
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2
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540
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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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463
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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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422
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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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482
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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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772
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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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508
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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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579
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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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527
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Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
3.0 years ago michael.weber.1 • 0
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1
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550
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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
views
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
748
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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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622
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TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
3.2 years ago Ina Hoeschele ▴ 610
50 results • Page 1 of 1
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Replies
Comment: Selecting pairs of exons from differentially spliced genes by jamie.gearing ▴ 40
That is fair enough. Sensible is always reassuring to hear! Thanks very much for your input Gordon. Best regards, Jamie.
Answer: Selecting pairs of exons from differentially spliced genes by Gordon Smyth 43k
Choosing a representative pair of exons is not part of our method, so we won't make any recommendations. You should choose the exons wit…
Comment: combineTwoExpressionSet from a4Base is not working properly by russ.bainer • 0
I ran across this bug as well- the issue is related to the code failing to reorder the ExpressionSet rows prior to merging. A workaround fo…
Comment: Best practice for quantifying sncRNA by Abhishek • 0
k has to be odd - trying 9, 21 instead
Comment: Best practice for quantifying sncRNA by Abhishek • 0
I did use the genome as decoy. And I used whole transcriptome from Gencode for indexing. Maybe I should index using just non coding transc…
Votes
Answer: Selecting pairs of exons from differentially spliced genes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
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