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
reply
439
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 5 months ago by 66k • written 5 months ago by • 0
0
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1
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485
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
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489
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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
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781
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 12 months ago by 16k • written 12 months ago by • 0
1
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0
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481
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
13 months ago Shreyash ▴ 10
4
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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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846
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
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5
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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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473
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
19 months ago nattzy94 ▴ 20
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2
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1.0k
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
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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
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5
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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
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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
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3.6k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.3 years ago • updated 2.2 years ago rbenel ▴ 40
0
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1
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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
1.0k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
2
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2
replies
908
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 2.5 years ago by 16k • written 2.5 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
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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
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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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856
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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818
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
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2
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1.7k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
3.3 years ago erhoppe • 0
5
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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
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1
reply
712
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
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1.2k
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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
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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
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1
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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
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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
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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
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979
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
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821
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
904
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: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Comment: Error in render R qmd document (could not find function "process") by ATpoint ★ 4.2k
This is not related to Bioconductor, and even if it was, please understand that without code one cannot debug these questions. The most obv…
Comment: GSVA function by michelafrancesconi8 • 0
When I log trasform my matrix after the DESeq2 normalization, I have some negative value, should I add a 1 to all my matrix? Thank you Mi…
Comment: Normalisation using clinical traits in RNA seq using DESeq2 by sukeshinik5 • 0
Thank you, so much for the response. When we estimate factors of unwanted variable, which is the better options for factorisation of the va…
Votes
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
C: DiffBind Batch Effect
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