Showing : GenomicFeatures • reset
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Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 5 months ago by 66k • written 5 months ago by ▴ 10
2
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1
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584
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Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 7 months ago by 66k • written 7 months ago by • 0
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583
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How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
9 months ago rohitsatyam102 ▴ 20
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3
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2.2k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 10 months ago by 51k • written 10 months ago by • 0
2
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2
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550
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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
13 months ago gernophil • 0
1
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4
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850
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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 14 months ago by 16k • written 14 months ago by • 0
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0
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531
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Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
15 months ago Shreyash ▴ 10
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8
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1.7k
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
16 months ago davidhillis • 0
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2
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945
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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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1.4k
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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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520
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Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
21 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 22 months ago by 42k • written 22 months ago by ▴ 10
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4
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2.3k
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error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 2.2 years ago by 16k • written 2.2 years ago by • 0
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9
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1.8k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 24 months ago by 42k • written 2.3 years ago by • 0
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18
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3.9k
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Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.5 years ago • updated 2.4 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 2.6 years ago by ▴ 30
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2
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1.4k
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.7 years ago Madza Farias-Virgens • 0
2
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3
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2.8k
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How to get longest isoform
GenomicFeatures Biostrings
updated 2.7 years ago by 16k • written 2.7 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
2.7 years ago Madza Farias-Virgens • 0
2
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2
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973
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 2.7 years ago by 16k • written 2.7 years ago by • 0
5
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2
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1.2k
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How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
2.9 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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1.6k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
3.0 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
3.0 years ago A.J. ▴ 20
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0
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970
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.0 years ago Matthias Munz ▴ 10
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0
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865
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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
3.5 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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3.3k
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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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753
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.5 years ago by ▴ 80 • written 3.8 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 4.0 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 4.0 years ago by 66k • written 4.0 years ago by ▴ 30
0
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1
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1.3k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 4.0 years ago by 3.9k • written 4.0 years ago by • 0
3
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6
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2.2k
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
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 4.2 years ago by 66k • written 4.2 years ago by ▴ 100
0
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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 4.2 years ago by ★ 11k • written 4.2 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
0
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2
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893
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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1.9k
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
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how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 4.3 years ago by 16k • written 4.4 years ago by ▴ 40
1
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2
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955
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.4 years ago by ★ 13k • written 4.4 years ago by ▴ 40
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0
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1.0k
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 4.5 years ago by 66k • written 4.5 years ago by • 0
8
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12
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5.8k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.0 years 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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1.0k
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 4.6 years ago by ★ 11k • written 4.6 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 4.7 years ago by 16k • written 4.7 years ago by ▴ 90
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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