Showing : genomicfeatures • reset
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Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 3 months ago by 66k • written 3 months ago by ▴ 10
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 4 months ago by ▴ 10 • written 8.5 years ago by ▴ 10
2
votes
1
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449
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 5 months ago by 66k • written 5 months ago by • 0
0
votes
1
reply
490
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
7 months ago rohitsatyam102 ▴ 20
2
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3
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1.8k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 8 months ago by 50k • written 8 months ago by • 0
2
votes
2
replies
489
views
Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
9 months ago Geert ▴ 10
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2
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1.0k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
11 months ago gernophil • 0
1
vote
4
replies
786
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 12 months ago by 16k • written 12 months ago by • 0
1
vote
0
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485
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
13 months ago Shreyash ▴ 10
4
votes
8
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1.5k
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation
14 months ago davidhillis • 0
0
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2
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852
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
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5
replies
1.3k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 17 months ago by 66k • written 17 months ago by • 0
0
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0
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474
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
19 months ago nattzy94 ▴ 20
0
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2
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1.1k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 20 months ago by 42k • written 20 months ago by ▴ 10
5
votes
9
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1.6k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 22 months ago by 42k • written 2.1 years ago by • 0
4
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3
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2.0k
views
How to extract only mRNA from TxDb object?
genomicfeatures
updated 22 months ago by ▴ 40 • written 7.6 years ago by ▴ 50
8
votes
12
replies
5.6k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 22 months ago by • 0 • written 9.2 years ago by ▴ 20
0
votes
4
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2.1k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 2.0 years ago by 16k • written 2.0 years ago by • 0
6
votes
5
replies
4.8k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 2.1 years ago by 16k • written 5.3 years ago by • 0
3
votes
3
replies
1.5k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 2.1 years ago by 66k • written 2.4 years ago by ▴ 30
0
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18
replies
3.6k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.3 years ago rbenel ▴ 40
0
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1
reply
1.4k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 2.5 years ago by • 0 • written 8.5 years ago by ▴ 10
1
vote
2
replies
1.3k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
2
votes
3
replies
2.6k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
1
vote
2
replies
1.1k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
2
votes
2
replies
909
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 2.5 years ago by 16k • written 2.6 years ago by • 0
0
votes
3
replies
1.1k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 2.6 years ago by • 0 • written 3.6 years ago by ▴ 120
5
votes
2
replies
1.1k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
2.7 years ago Pratik Mehta ▴ 10
0
votes
1
reply
1.0k
views
install GenomicFeatures fail
GenomicFeatures install
updated 2.8 years ago by 66k • written 2.8 years ago by ▴ 80
1
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4
replies
1.5k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
2.8 years ago A.J. ▴ 20
1
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3
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1.1k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
2.8 years ago A.J. ▴ 20
0
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0
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861
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.8 years ago Matthias Munz ▴ 10
0
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0
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819
views
annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.1 years ago António Miguel de Jesus Domingues ▴ 510
0
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5
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2.8k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.2 years ago sieminsk • 0
2
votes
2
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1.7k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
3.3 years ago erhoppe • 0
5
votes
5
replies
1.9k
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 3.3 years ago by ★ 1.5k • written 4.8 years ago by ▴ 10
0
votes
1
reply
713
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.3 years ago by ▴ 80 • written 3.6 years ago by ▴ 10
0
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6
replies
1.2k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
3.3 years ago rproendo ▴ 20
0
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2
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3.1k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
0
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1
reply
4.5k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.8 years ago by 66k • written 3.8 years ago by ▴ 90
3
votes
7
replies
1.6k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 3.8 years ago by 66k • written 3.8 years ago by ▴ 30
0
votes
1
reply
1.2k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 3.8 years ago by 3.9k • written 3.8 years ago by • 0
3
votes
6
replies
2.0k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 3.9 years ago by 25k • written 3.9 years ago by ▴ 120
0
votes
1
reply
1.2k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 4.0 years ago by 66k • written 4.0 years ago by ▴ 100
0
votes
2
replies
1.1k
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
0
votes
0
replies
981
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
4.1 years ago Guandong Shang ▴ 40
0
votes
2
replies
825
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.1 years ago by 66k • written 4.1 years ago by ▴ 40
2
votes
3
replies
1.8k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 4.2 years ago by 66k • written 4.2 years ago by ▴ 100
3
votes
4
replies
1.1k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 4.2 years ago by 16k • written 4.2 years ago by ▴ 40
1
vote
2
replies
906
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.2 years ago by ★ 13k • written 4.2 years ago by ▴ 40
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Comment: How to run allelic imbalance in apeglm by parayod376 • 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
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FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
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If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
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Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
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