Showing : Genomicfeatures • reset
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Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 4 months ago by 66k • written 4 months ago by ▴ 10
2
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1
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532
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Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 6 months ago by 66k • written 6 months ago by • 0
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537
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How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
8 months ago rohitsatyam102 ▴ 20
2
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3
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2.0k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 9 months ago by 51k • written 9 months ago by • 0
2
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2
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514
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Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
11 months ago Geert ▴ 10
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2
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1.1k
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What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
12 months ago gernophil • 0
1
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4
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818
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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 13 months ago by 16k • written 13 months ago by • 0
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0
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509
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Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
14 months ago Shreyash ▴ 10
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8
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1.6k
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
15 months ago davidhillis • 0
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2
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917
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how to match salmon output to txname
GenomicFeatures tximport salmon
written 18 months ago by • 0
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5
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1.3k
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Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 19 months ago by 66k • written 19 months ago by • 0
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495
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Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
20 months ago nattzy94 ▴ 20
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2
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1.1k
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How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 21 months ago by 42k • written 21 months ago by ▴ 10
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4
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2.2k
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error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 2.1 years ago by 16k • written 2.1 years ago by • 0
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9
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1.7k
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Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 23 months ago by 42k • written 2.2 years ago by • 0
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18
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3.8k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.4 years ago • updated 2.3 years ago rbenel ▴ 40
3
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3
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1.6k
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GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 2.2 years ago by 66k • written 2.5 years ago by ▴ 30
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2
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1.3k
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.6 years ago Madza Farias-Virgens • 0
2
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3
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2.7k
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How to get longest isoform
GenomicFeatures Biostrings
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
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2
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1.1k
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NAs in my txdb tx_name
GenomicFeatures Biostrings
2.6 years ago Madza Farias-Virgens • 0
2
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2
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939
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Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 2.6 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
2.8 years ago Pratik Mehta ▴ 10
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1
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1.1k
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install GenomicFeatures fail
GenomicFeatures install
updated 2.9 years ago by 66k • written 2.9 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
2.9 years ago A.J. ▴ 20
1
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3
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1.2k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
2.9 years ago A.J. ▴ 20
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0
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917
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.9 years ago Matthias Munz ▴ 10
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0
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839
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.2 years ago António Miguel de Jesus Domingues ▴ 510
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5
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2.9k
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.3 years ago sieminsk • 0
2
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2
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1.8k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
3.4 years ago erhoppe • 0
0
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6
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1.3k
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Splitting TxDb by Strand
GenomicFeatures TxDb
3.4 years ago rproendo ▴ 20
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3
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1.2k
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Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 2.7 years ago by • 0 • written 3.7 years ago by ▴ 120
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2
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3.2k
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Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
0
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1
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733
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.4 years ago by ▴ 80 • written 3.7 years ago by ▴ 10
0
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1
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4.7k
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Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.9 years ago by 66k • written 3.9 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 3.9 years ago by 66k • written 3.9 years ago by ▴ 30
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1
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1.3k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 3.9 years ago by 3.9k • written 3.9 years ago by • 0
3
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6
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2.1k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 4.0 years ago by 25k • written 4.0 years ago by ▴ 120
0
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1
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1.3k
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makeTxDbFromGFF warning meaning
GenomicFeatures
updated 4.1 years ago by 66k • written 4.1 years ago by ▴ 100
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2
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1.1k
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How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.1 years ago by ★ 11k • written 4.1 years ago by ▴ 10
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0
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1.0k
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
4.2 years ago Guandong Shang ▴ 40
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2
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857
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.2 years ago by 66k • written 4.2 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 4.3 years ago by 66k • written 4.3 years ago by ▴ 100
3
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4
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1.2k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 4.3 years ago by 16k • written 4.3 years ago by ▴ 40
1
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2
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927
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.3 years ago by ★ 13k • written 4.3 years ago by ▴ 40
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0
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985
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 4.4 years ago by 3.9k • written 4.4 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 4.4 years ago by 66k • written 4.4 years ago by • 0
8
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12
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5.7k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 23 months ago by • 0 • written 9.3 years ago by ▴ 20
2
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3
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1.2k
views
GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 4.5 years ago by 66k • written 4.5 years ago by ▴ 30
0
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3
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989
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 4.5 years ago by ★ 11k • written 4.5 years ago by ▴ 90
0
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8
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1.8k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 4.6 years ago by 16k • written 4.6 years ago by ▴ 90
50 results • Page 1 of 1
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Answer: Most sensible approach to a `stage*condition` design in DESeq2 by swbarnes2 ★ 1.4k
Doing a stage_treatment grouping is not the same as doing stage * treatment. You can use stage * treatment to compare one subgroup to anot…
Comment: Ranking the GSEA Results by Lluís Revilla Sancho ▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction by Antonio • 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results by alserg ▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results by alserg ▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Votes
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
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