Showing : genomicfeatures • reset
0
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4
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error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 11 weeks ago by 15k • written 11 weeks ago by • 0
5
votes
9
replies
430
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 10 days ago by 37k • written 4 months ago by • 0
0
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18
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1.2k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
6 months ago • updated 5 months ago rbenel ▴ 20
3
votes
3
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587
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 3 months ago by 60k • written 7 months ago by ▴ 20
1
vote
2
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407
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
8 months ago Madza Farias-Virgens • 0
2
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3
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557
views
How to get longest isoform
GenomicFeatures Biostrings
updated 9 months ago by 15k • written 9 months ago by • 0
1
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2
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322
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
9 months ago Madza Farias-Virgens • 0
2
votes
2
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298
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 9 months ago by 15k • written 9 months ago by • 0
5
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2
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427
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
11 months ago Pratik Mehta ▴ 10
0
votes
1
reply
340
views
install GenomicFeatures fail
GenomicFeatures install
updated 11 months ago by 60k • written 11 months ago by ▴ 80
1
vote
4
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425
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
12 months ago A.J. ▴ 20
1
vote
3
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360
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
12 months ago A.J. ▴ 20
0
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0
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242
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
12 months ago Matthias Munz ▴ 10
0
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0
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280
views
annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
15 months ago António Miguel de Jesus Domingues ▴ 490
0
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5
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943
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
16 months ago sieminsk • 0
2
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2
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635
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
17 months ago erhoppe • 0
0
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6
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528
views
Splitting TxDb by Strand
GenomicFeatures TxDb
18 months ago rproendo ▴ 20
0
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3
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377
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 9 months ago by • 0 • written 21 months ago by ▴ 100
0
votes
2
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1.2k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 21 months ago by 37k • written 21 months ago by • 0
0
votes
1
reply
323
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 18 months ago by ▴ 80 • written 22 months ago by ▴ 10
0
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1
reply
1.6k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 24 months ago by 60k • written 24 months ago by ▴ 90
3
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7
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771
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 2.0 years ago by 60k • written 2.0 years ago by ▴ 10
0
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1
reply
506
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 2.0 years ago by 3.2k • written 2.0 years ago by • 0
3
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6
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624
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 2.1 years ago by 25k • written 2.1 years ago by ▴ 120
0
votes
1
reply
371
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 2.2 years ago by 60k • written 2.2 years ago by ▴ 100
0
votes
2
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349
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 2.2 years ago by 11k • written 2.2 years ago by ▴ 10
0
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0
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400
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
2.3 years ago Guandong Shang ▴ 20
0
votes
2
replies
259
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 2.3 years ago by 60k • written 2.3 years ago by ▴ 30
2
votes
3
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789
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 2.4 years ago by 60k • written 2.4 years ago by ▴ 80
3
votes
4
replies
522
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 2.4 years ago by 15k • written 2.4 years ago by ▴ 20
1
vote
2
replies
392
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 2.4 years ago by 13k • written 2.4 years ago by ▴ 40
0
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0
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362
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 2.5 years ago by 3.2k • written 2.5 years ago by • 0
0
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2
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467
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 2.5 years ago by 60k • written 2.5 years ago by • 0
8
votes
12
replies
3.6k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 27 days ago by • 0 • written 7.4 years ago by ▴ 20
2
votes
3
replies
353
views
GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 2.6 years ago by 60k • written 2.6 years ago by ▴ 10
0
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3
replies
448
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 2.6 years ago by 11k • written 2.6 years ago by ▴ 90
0
votes
8
replies
627
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 2.8 years ago by 15k • written 2.8 years ago by ▴ 90
0
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0
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334
views
SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
2.8 years ago rmash • 0
4
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3
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1.7k
views
TxDb error: external pointer is not valid
software error GenomicFeatures
2.9 years ago O. William McClung • 0
0
votes
2
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576
views
Error while creating txDb from gtf file
genomicfeatures
3.0 years ago bioinagesh • 0
5
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5
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770
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 18 months ago by ★ 1.5k • written 3.0 years ago by ▴ 10
0
votes
1
reply
539
views
create a full TXDB object from GFF3 data for a non-system organism / denovo assembly
GenomicFeatures rtracklayer
updated 3.3 years ago by 15k • written 3.3 years ago by ▴ 10
0
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0
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764
views
error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
3.3 years ago xvazquezc • 0
0
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0
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392
views
Features function from genomicFeatures package worked in 2014 but currently doesn't work (upload of a deleted post)
genomicfeatures
updated 3.4 years ago by 25k • written 3.4 years ago by • 0
4
votes
5
replies
1.8k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 3 months ago by 15k • written 3.5 years ago by • 0
5
votes
6
replies
1.1k
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 3.5 years ago by 15k • written 3.6 years ago by • 0
0
votes
5
replies
554
views
GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures bug
updated 3.7 years ago by 60k • written 3.7 years ago by ★ 1.6k
1
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2
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702
views
makeTxDbFromUCSC: error in Make the TxDb object
GenomicFeatures makeTxDbFromUCSC R
3.8 years ago DMA1 ▴ 10
0
votes
2
replies
612
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
3.8 years ago A ▴ 40
0
votes
1
reply
570
views
NCBI hg38 transcript annotation package GenomicFeatures
GenomicFeatures
updated 3.8 years ago by 60k • written 3.8 years ago by • 0
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Comment: IsoformSwitchAnalyzeR package on mouse data by bpshtiwan ▴ 10
Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem? Best
Comment: Design and contrast matrices for analyzing the effect of two factors of interest by Gordon Smyth 46k
I understand that your mock dataset has expression data for just one protein instead of 8000, but is the phenoData complete? Does your real…
Comment: error running UniProt.ws by James W. MacDonald 60k
Or maybe it is a quick fix! Nicely done Marcel!
Answer: Error with TCGA package - TCGAbiolinks by Tiago C. Silva ▴ 220
It is working with the github version. Could you update please? BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data") …
Comment: Error with TCGA package - TCGAbiolinks by Marcel Ramos 570
You can try the Genomic Data Commons Data Portal at [https://portal.gdc.cancer.gov/][1] or the `GenomicDataCommons` R/Bioconductor packag…
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A: Importance of Order in Design Formula
remove microarray batch effects using Limma
On empirical Bayes of edgeR
Answer: CQN to DESeq2
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
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