Showing : Genomicfeatures • reset
2
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GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 30
0
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3
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1.2k
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Resize exons in transcript to total width
genomicranges genomicfeatures
updated 5.7 years ago by ★ 11k • written 5.7 years ago by ▴ 90
0
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8
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2.5k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 90
2
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0
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1.1k
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
5.8 years ago rmash ▴ 20
4
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3
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3.9k
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TxDb error: external pointer is not valid
software error GenomicFeatures
5.9 years ago O. William McClung • 0
0
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2
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1.4k
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Error while creating txDb from gtf file
genomicfeatures
6.0 years ago bioinagesh • 0
5
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5
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2.7k
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threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 4.5 years ago by ★ 1.6k • written 6.0 years ago by ▴ 10
0
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1
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1.5k
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create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 6.3 years ago by 16k • written 6.3 years ago by ▴ 10
0
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0
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1.9k
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error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
6.4 years ago xvazquezc • 0
0
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0
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880
views
Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
6
votes
5
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6.8k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 3.3 years ago by 16k • written 6.6 years ago by • 0
5
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6
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4.3k
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 6.6 years ago by 16k • written 6.6 years ago by • 0
0
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5
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1.3k
views
GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 6.8 years ago by 68k • written 6.8 years ago by ★ 1.6k
1
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2
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1.9k
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makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
6.8 years ago DMA1 ▴ 10
0
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2
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1.3k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
6.9 years ago A ▴ 60
0
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1
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1.1k
views
NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
0
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0
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1.7k
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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
6.9 years ago Wojeff • 0
1
vote
8
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3.4k
views
Trying to map nucleotide position from a transcript to genomic location
genomicfeatures mapfromtranscripts mirna
updated 7.0 years ago by ★ 6.8k • written 7.0 years ago by ▴ 20
0
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1
reply
2.1k
views
getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was truncated"
getPromoterSeq GRanges GenomicFeatures
7.0 years ago jerrywu1987 • 0
1
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1
reply
3.1k
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 7.1 years ago by ▴ 20 • written 7.1 years ago by • 0
0
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1
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1.6k
views
getting mouse gene ids from makeTxDbFromUCSC()
GenomicFeatures makeTxDbFromUCSC
updated 7.1 years ago by 4.2k • written 7.1 years ago by • 0
0
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5
replies
1.6k
views
Custom BSgenome with makeTxDbFromGFF
bsgenome genomicfeatures
7.1 years ago michael.weber.1 • 0
0
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1
reply
1.8k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 7.1 years ago by ▴ 50 • written 7.2 years ago by • 0
1
vote
1
reply
972
views
makeTxdbFromUCSC fails to download
maketxdbpackagefromucsc rtracklayer genomicfeatures
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
1
reply
3.2k
views
TxDb.Hsapiens.UCSC.hg19.knownGen installation fail - non-zero exit status
software error package installation genomicfeatures
updated 7.2 years ago by 25k • written 7.2 years ago by • 0
3
votes
1
reply
3.5k
views
How does GenomicFeature calculate 3'UTR?
genomicfeatures annotation utr
updated 7.2 years ago by 16k • written 7.2 years ago by • 0
1
vote
3
replies
2.2k
views
GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
genomicfeatures
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 30
0
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1
reply
1.9k
views
TPM and FPKM for lncRNA
GenomicFeatures TPM FPKM lncRNA
7.3 years ago Ina Hoeschele ▴ 620
0
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2
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1.3k
views
Cannot get TxDb object using makeTxDbFromUCSC in any table:
software error genomicfeatures
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
1
vote
1
reply
1.4k
views
installation of "GenomicFeatures"
GenomicFeatures
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
1
vote
14
replies
4.2k
views
DEXSeq - dexseq_count.py issue
dexseq dexseq_count genomicfeatures
updated 7.4 years ago by • 0 • written 7.5 years ago by • 0
0
votes
1
reply
1000
views
Setting up PLAYRDesign gives error on makeTxDbFromUCSC, error in tableNames
genomicfeatures R
7.4 years ago songshan.guo • 0
5
votes
5
replies
2.8k
views
makeTxDbFromUCSC("hg19", "refGene") gives "not supported" error
genomicfeatures
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 20
0
votes
1
reply
1.3k
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
7.5 years ago lucasmacielbiotec • 0
2
votes
2
replies
1.7k
views
Get canonical exon locations for gene
genomicfeatures r bioconductor
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
1
vote
5
replies
2.5k
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Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 7.5 years ago by 16k • written 7.5 years ago by ▴ 50
0
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2
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1.9k
views
circular genome visualisation: genomic.labels: Error in if (cr != chr) { : missing value where TRUE/FALSE needed
genomicfeatures rcircos
7.6 years ago chrisclarkson100 ▴ 50
0
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2
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1.2k
views
Error with makeTxDbFromBiomart in GenomicFeatures package
genomicfeatures
updated 7.6 years ago by 16k • written 7.6 years ago by • 0
1
vote
4
replies
2.1k
views
Genomic Features UCSC refseq genes "Download the knownGene table ... Error: Bad Request"
genomicfeatures
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 30
1
vote
3
replies
1.8k
views
how to get intron with ensembldb. package?
granges ensembldb GenomicFeatures
7.6 years ago alessandro.pastore ▴ 20
3
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1
reply
1.0k
views
Error in makeTxDbFromBiomart for fungi_mart
genomicfeatures biomart
7.6 years ago JohnTownsend ▴ 20
3
votes
6
replies
2.5k
views
cummeRbund installation fails
bioconductor cummerbund software error GenomicFeatures
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 30
0
votes
2
replies
1.2k
views
How to specify transcript_ids in makeTxDbFromUCSC function in GenomicFeatures package?
genomicfeatures maketxdbfromucsc
7.7 years ago rbacher ▴ 20
2
votes
4
replies
2.7k
views
possible Rtracklayer issue: TxDb errors in GenomicFeatures package-- cannot load TxDb with standard params from UCSC (issue began last night)
genomicfeatures txdb maketxdbfromucsc maketxdbfrombiomart rtracklayer
updated 7.7 years ago by ★ 11k • written 7.7 years ago by ▴ 30
0
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0
replies
935
views
Missing Information with transcriptlengthsfunction
bioconductor genomicfeatures rtracklayer transriptlengths
7.7 years ago michael.soutschek • 0
0
votes
5
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1.8k
views
makeTxdbFromUCSC in genomicfeatures package is broken
genomicfeatures
updated 7.7 years ago by ★ 11k • written 7.7 years ago by • 0
2
votes
2
replies
2.5k
views
Intron length per transcript using GenomicFeatures
intron GenomicFeatures
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 10
0
votes
2
replies
1.2k
views
GRangesList: wiered error
genomicranges genomicfeatures
7.8 years ago Fabian Grammes ▴ 20
2
votes
4
replies
2.1k
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ★ 3.4k
2
votes
4
replies
2.3k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 7.8 years ago by 16k • written 7.9 years ago by ▴ 40
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Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
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I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
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It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
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Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
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Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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