Showing : txdb • reset
0
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440
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How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
6 months ago rohitsatyam102 ▴ 20
2
votes
5
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673
views
bambu output
txdb bambu
updated 10 months ago by ▴ 20 • written 10 months ago by • 0
0
votes
0
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578
views
Identify accepted columns in TxDb objects
TxDb
15 months ago Lluís Revilla Sancho ▴ 730
0
votes
1
reply
558
views
TxDb conversion of transcript id to gene id
TxDb.Sscrofa.UCSC.susScr11.refGene TxDb txi
updated 17 months ago by 65k • written 17 months ago by • 0
3
votes
5
replies
1.8k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 2.4 years ago by 16k • written 2.4 years ago by ▴ 40
5
votes
6
replies
2.0k
views
NA transcript values in my Txdb
GFF txdb
updated 2.4 years ago by 65k • written 2.5 years ago by ▴ 20
1
vote
7
replies
2.1k
views
How to get annotations for all genes that overlap a region with annotatePeak
txdb R annotatation
2.8 years ago pegah.taklifi ▴ 30
0
votes
5
replies
2.7k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.1 years ago sieminsk • 0
0
votes
6
replies
1.2k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
3.2 years ago rproendo ▴ 20
0
votes
3
replies
1.0k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 2.5 years ago by • 0 • written 3.5 years ago by ▴ 120
0
votes
1
reply
4.4k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 90
0
votes
5
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1.4k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
3
votes
6
replies
1.9k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 3.8 years ago by 25k • written 3.8 years ago by ▴ 120
3
votes
6
replies
1.1k
views
Extremely big genes in annotation TxDb packages
annotation txdb AnnotationData Genetics
updated 3.8 years ago by 65k • written 3.8 years ago by ▴ 10
0
votes
2
replies
805
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation software TxDb
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
0
votes
0
replies
844
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
3.9 years ago hfyuan2016 • 0
0
votes
2
replies
1.0k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.0 years ago by ★ 11k • written 4.0 years ago by ▴ 10
1
vote
2
replies
877
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.1 years ago by ★ 13k • written 4.1 years ago by ▴ 40
0
votes
2
replies
972
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
0
votes
5
replies
1.9k
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 4.2 years ago by 41k • written 4.2 years ago by • 0
6
votes
5
replies
1.0k
views
PTEN missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
TxDb annotation TxDb.Hsapiens.UCSC.hg38.knownGene
updated 4.3 years ago by 3.8k • written 4.3 years ago by ▴ 150
6
votes
4
replies
2.6k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 4.7 years ago by 25k • written 4.7 years ago by ▴ 670
2
votes
5
replies
2.1k
views
Warning in makeTxDbFromGFF
txdb
updated 3.1 years ago by 16k • written 4.9 years ago by ▴ 10
2
votes
1
reply
879
views
Do TxDb objects contain info about non-transcriptionally active regions?
TxDb GRanges BSGenome variant annotation
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 40
3
votes
2
replies
1.7k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 5.2 years ago by ★ 2.0k • written 5.2 years ago by ▴ 100
2
votes
4
replies
1.4k
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 5.4 years ago by 65k • written 5.4 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Error in makeTxDbFromBiomart
software error txdb maketxdbfrombiomart
5.5 years ago katie_emelianova • 0
0
votes
1
reply
1.3k
views
makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
genomicfeatures txdb maketxdbfromgff
updated 5.8 years ago by ▴ 50 • written 5.8 years ago by • 0
0
votes
1
reply
1.0k
views
TxDb basic question
txdb TxDb.Mmulatta.UCSC.rheMac8.refGene
updated 5.8 years ago by ▴ 50 • written 5.8 years ago by ▴ 120
0
votes
4
replies
1.7k
views
Merging each element of a list of Genomic range
txdb granges cds orf R
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
1
reply
1.0k
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
6.1 years ago lucasmacielbiotec • 0
1
vote
5
replies
1.9k
views
Extract genomic features from a TxDb-like object
TxDB genomicfeatures promoter getpromoterseq
updated 6.1 years ago by 16k • written 6.1 years ago by ▴ 40
0
votes
1
reply
3.9k
views
create a txdb using makeTxDbFromGFF
bioconductor txdb maketxdbfromgff
6.4 years ago Nader.Aryamanesh • 0
2
votes
4
replies
2.1k
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 6.4 years ago by ★ 11k • written 6.4 years ago by ▴ 30
2
votes
2
replies
4.4k
views
How to prepare TxDb object using makeTxDbFromGFF with polycistronic transcripts?
txdb gff3 polycistronic transcript
6.5 years ago Piotr Gawronski • 0
0
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0
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1.3k
views
News: OrgDb and TxDb packages have been added to AnnotationHub for Bioc 3.6
orgdb txdb bioconductor annotation annotationhub News
6.5 years ago shepherl 3.8k
0
votes
4
replies
1.6k
views
Cannot extract TxFeatures for a defined GRanges object
TxDB genomicranges genomicfeatures
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 10
0
votes
2
replies
1.5k
views
Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
txdb txdb.hsapiens.ucsc.hg19.knowngene gviz
updated 6.5 years ago by 65k • written 6.5 years ago by ▴ 10
4
votes
5
replies
1.5k
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 6.6 years ago by ▴ 180 • written 6.6 years ago by ▴ 10
0
votes
2
replies
2.0k
views
add annotation features to BSgenome or txdb package
bsgenome txdb annotation orgdb
6.8 years ago • updated 6.7 years ago Didi ▴ 10
0
votes
2
replies
1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
0
votes
1
reply
1.2k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 7.1 years ago by 65k • written 7.1 years ago by • 0
5
votes
7
replies
1.9k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 7.1 years ago by 65k • written 7.1 years ago by ▴ 40
2
votes
1
reply
1.1k
views
makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
genomicfeatures txdb
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 40
0
votes
2
replies
1.3k
views
Error in TxDb mm10 coordinates?
txdb txdb.mmusculus.ucsc.mm10.knowngene
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 10
3
votes
3
replies
1.3k
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 7.7 years ago by 25k • written 7.7 years ago by ▴ 450
1
vote
2
replies
2.5k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 7.8 years ago by 16k • written 7.8 years ago by ★ 3.9k
4
votes
2
replies
1.3k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 8.0 years ago by ★ 6.8k • written 8.0 years ago by ▴ 80
0
votes
5
replies
1.6k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
8.0 years ago TimothéeFlutre ▴ 80
0
votes
2
replies
1.2k
views
how to get transcript annotation (unique)
txdb
8.0 years ago KB ▴ 50
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
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C: when to apply quantile normalization with voom in limma/voom framework with RNA-
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Answer: Log-cpm values from limma
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