Showing : txdb • reset
0
votes
0
replies
80
views
Identify accepted columns in TxDb objects
TxDb
5 weeks ago • updated 29 days ago Lluís Revilla Sancho ▴ 710
0
votes
1
reply
155
views
TxDb conversion of transcript id to gene id
TxDb.Sscrofa.UCSC.susScr11.refGene TxDb txi
updated 3 months ago by 62k • written 3 months ago by • 0
3
votes
5
replies
892
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 14 months ago by 16k • written 14 months ago by ▴ 40
4
votes
6
replies
1.0k
views
NA transcript values in my Txdb
GFF txdb
updated 15 months ago by 62k • written 16 months ago by ▴ 20
1
vote
7
replies
924
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
19 months ago pegah.taklifi ▴ 30
0
votes
5
replies
1.4k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
22 months ago sieminsk • 0
0
votes
6
replies
664
views
Splitting TxDb by Strand
GenomicFeatures TxDb
2.0 years ago rproendo ▴ 20
0
votes
3
replies
512
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 15 months ago by • 0 • written 2.3 years ago by ▴ 120
0
votes
1
reply
2.4k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 2.5 years ago by 62k • written 2.5 years ago by ▴ 90
0
votes
5
replies
819
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 2.5 years ago by 39k • written 2.5 years ago by • 0
3
votes
6
replies
884
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 2.6 years ago by 25k • written 2.6 years ago by ▴ 120
3
votes
6
replies
645
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 2.6 years ago by 62k • written 2.6 years ago by ▴ 10
0
votes
2
replies
419
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 2.7 years ago by 62k • written 2.7 years ago by • 0
0
votes
0
replies
491
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
2.7 years ago hfyuan2016 • 0
0
votes
2
replies
483
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 2.7 years ago by 11k • written 2.7 years ago by ▴ 10
1
vote
2
replies
484
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 2.9 years ago by 13k • written 2.9 years ago by ▴ 40
0
votes
2
replies
568
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 3.0 years ago by 62k • written 3.0 years ago by • 0
0
votes
5
replies
951
views
Changing Gene ID annotation style - working with Salmon output [NM...] and resulting count files are numeric-only IDs
tximport Gene IDs txdb RefSeq Salmon
updated 3.0 years ago by 39k • written 3.0 years ago by • 0
6
votes
5
replies
508
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 3.0 years ago by 3.4k • written 3.0 years ago by ▴ 150
6
votes
4
replies
1.5k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 3.5 years ago by 25k • written 3.5 years ago by ▴ 660
2
votes
5
replies
1.3k
views
Warning in makeTxDbFromGFF
txdb
updated 22 months ago by 16k • written 3.6 years ago by ▴ 10
2
votes
1
reply
544
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 3.9 years ago by 62k • written 3.9 years ago by ▴ 40
3
votes
2
replies
1.1k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 4.0 years ago by ★ 2.0k • written 4.0 years ago by ▴ 80
2
votes
4
replies
895
views
Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.knownGene: incorrect number of exons and overlapping exons
txdb txdb.hsapiens.ucsc.hg19.knowngene granges exons ucsc
updated 4.2 years ago by 62k • written 4.2 years ago by ▴ 10
0
votes
3
replies
967
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
4.3 years ago katie_emelianova • 0
0
votes
1
reply
886
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 4.6 years ago by ▴ 50 • written 4.6 years ago by • 0
0
votes
1
reply
660
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 4.6 years ago by ▴ 50 • written 4.6 years ago by ▴ 120
0
votes
4
replies
1.1k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 4.7 years ago by 62k • written 4.7 years ago by • 0
0
votes
1
reply
767
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
4.9 years ago lucasmacielbiotec • 0
1
vote
5
replies
1.3k
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 4.9 years ago by 16k • written 4.9 years ago by ▴ 20
0
votes
1
reply
2.8k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
5.2 years ago Nader.Aryamanesh • 0
2
votes
4
replies
1.5k
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 5.2 years ago by 11k • written 5.2 years ago by ▴ 30
2
votes
2
replies
2.8k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
5.3 years ago Piotr Gawronski • 0
0
votes
4
replies
1.1k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 5.3 years ago by 16k • written 5.3 years ago by ▴ 10
0
votes
0
replies
877
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
5.3 years ago shepherl 3.4k
0
votes
2
replies
1.0k
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 5.3 years ago by 62k • written 5.3 years ago by ▴ 10
3
votes
5
replies
993
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 5.4 years ago by ▴ 150 • written 5.4 years ago by ▴ 10
0
votes
2
replies
1.5k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
5.6 years ago • updated 5.5 years ago Didi ▴ 10
0
votes
2
replies
1.2k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 5.6 years ago by 39k • written 5.6 years ago by • 0
0
votes
1
reply
933
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 5.8 years ago by 62k • written 5.8 years ago by • 0
5
votes
7
replies
1.4k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 5.9 years ago by 62k • written 5.9 years ago by ▴ 30
2
votes
1
reply
847
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 6.2 years ago by 62k • written 6.2 years ago by ▴ 40
0
votes
2
replies
859
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 6.2 years ago by 62k • written 6.2 years ago by ▴ 10
3
votes
3
replies
944
views
Genes found on particular chromosome using two methods in TxDb.Hsapiens.UCSC.hg19.knownGene were not identical
txdb.hsapiens.ucsc.hg19.knowngene txdb
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 450
1
vote
2
replies
2.0k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 6.6 years ago by 16k • written 6.6 years ago by ★ 3.5k
4
votes
2
replies
937
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 6.8 years ago by ★ 6.7k • written 6.8 years ago by ▴ 80
0
votes
5
replies
1.0k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
6.8 years ago TimothéeFlutre ▴ 80
0
votes
2
replies
915
views
how to get transcript annotation (unique)
txdb
6.8 years ago KB ▴ 50
7
votes
4
replies
2.9k
views
PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
txdb txdb.hsapiens.ucsc.hg19.knowngene txdb.hsapiens.ucsc.hg38.knowngene org.hs.eg.db annotation
6.8 years ago enricoferrero ▴ 650
0
votes
0
replies
875
views
extractUpstreamSeqs with custom genome, no gene_id shown
genomicranges txdb genomicfeatures featureextraction
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: DESeq2 and heatmap for multiple comparisons by artem.vorobyev • 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets by nicklesteele532 • 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions? by Hervé Pagès 16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons by swbarnes2 ★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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