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
2
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1
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450
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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491
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
10 months ago • updated 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
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4
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786
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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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485
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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852
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how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 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 18 months ago by • 0
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0
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475
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
0
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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
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 2.2 years ago by • 0
0
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18
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3.6k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.3 years ago rbenel ▴ 40
3
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3
replies
1.6k
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
1
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2
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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
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3
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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
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2
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1.1k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.5 years ago Madza Farias-Virgens • 0
2
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2
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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
5
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2
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1.1k
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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
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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862
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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
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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
0
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6
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1.2k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
3.3 years ago rproendo ▴ 20
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3
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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
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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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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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
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7
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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
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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
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1.2k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 4.0 years ago by 66k • written 4.0 years ago by ▴ 100
0
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2
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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
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0
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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
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2
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826
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.1 years ago by 66k • written 4.1 years ago by ▴ 40
2
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3
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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
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4
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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
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2
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908
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.2 years ago by ★ 13k • written 4.2 years ago by ▴ 40
0
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0
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958
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 4.3 years ago by 3.9k • written 4.3 years ago by • 0
0
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2
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1.0k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.3 years ago by 66k • written 4.3 years ago by • 0
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
2
votes
3
replies
1.1k
views
GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 4.4 years ago by 66k • written 4.4 years ago by ▴ 30
0
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3
replies
956
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 4.4 years ago by ★ 11k • written 4.4 years ago by ▴ 90
0
votes
8
replies
1.7k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 90
50 results • Page 1 of 1
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Comment: Deseq2 by Ram ▴ 210
Cross-posted on biostars: https://www.biostars.org/p/9596031/
Comment: SpliceWiz collateData error by giulia.nicoletto.1 • 0
Hi there, I am facing a similar error. When I try the collateData command collateData( Experiment = expr, reference_path = "./Referen…
Answer: Best way to describe DEseq2 design by SamGG ▴ 350
Hi, My own opinion. In the design `~ Batch`, ChemicalA_t1 is the intercept. So, all coefficients refer to this level as a reference. …
Answer: Deseq2 by ATpoint ★ 4.2k
Ser the vignette https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html It covers prefiltering (and everyt…
Comment: Counter-directional LFC shrinkage by Michael Love 42k
Gene 1 is hard to predict given the paucity of data for the comparison of interest. What is happening is that the relatively low dispersion…
Votes
Answer: Deseq2
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: When should I correct for batch effects
Answer: When should I correct for batch effects
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