Showing : genomicfeatures • reset
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Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 10 weeks ago by 65k • written 10 weeks ago by ▴ 10
2
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1
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386
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Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 4 months ago by 65k • written 4 months ago by • 0
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442
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How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
6 months ago rohitsatyam102 ▴ 20
2
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3
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1.5k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
2
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2
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453
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Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
8 months ago Geert ▴ 10
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2
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906
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What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
10 months ago gernophil • 0
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4
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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 10 months ago by 16k • written 11 months ago by • 0
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434
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Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
12 months ago Shreyash • 0
4
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8
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1.4k
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
13 months ago davidhillis • 0
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2
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782
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how to match salmon output to txname
GenomicFeatures tximport salmon
written 15 months ago by • 0
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5
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1.2k
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Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 16 months ago by 65k • written 16 months ago by • 0
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450
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Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
18 months ago nattzy94 ▴ 20
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2
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1.0k
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How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 19 months ago by 41k • written 19 months ago by ▴ 10
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4
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2.0k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 23 months ago by 16k • written 23 months ago by • 0
5
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9
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Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 21 months ago by 41k • written 2.1 years ago by • 0
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18
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3.5k
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Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.2 years ago rbenel ▴ 40
3
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3
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1.5k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 24 months ago by 65k • written 2.3 years ago by ▴ 30
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2
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1.2k
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
2.4 years ago Madza Farias-Virgens • 0
2
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3
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2.5k
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How to get longest isoform
GenomicFeatures Biostrings
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
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2
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1.0k
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NAs in my txdb tx_name
GenomicFeatures Biostrings
2.4 years ago Madza Farias-Virgens • 0
2
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2
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885
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Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 2.4 years ago by 16k • written 2.5 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
2.6 years ago Pratik Mehta ▴ 10
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1
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1000
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install GenomicFeatures fail
GenomicFeatures install
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 80
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4
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1.4k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
2.7 years ago A.J. ▴ 20
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3
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1.1k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
2.7 years ago A.J. ▴ 20
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0
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811
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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
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.0 years ago António Miguel de Jesus Domingues ▴ 490
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5
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2.7k
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.1 years ago sieminsk • 0
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2
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1.7k
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makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
3.2 years ago erhoppe • 0
0
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6
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1.2k
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Splitting TxDb by Strand
GenomicFeatures TxDb
3.2 years ago rproendo ▴ 20
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3
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1.1k
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Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 2.5 years ago by • 0 • written 3.5 years ago by ▴ 120
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2
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3.1k
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Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 3.5 years ago by 41k • written 3.5 years ago by • 0
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698
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.2 years ago by ▴ 80 • written 3.5 years ago by ▴ 10
0
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1
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4.4k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 90
3
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7
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1.5k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 30
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1.2k
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error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 3.7 years ago by 3.8k • written 3.7 years ago by • 0
3
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6
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1.9k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 3.8 years ago by 25k • written 3.8 years ago by ▴ 120
0
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1
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1.2k
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makeTxDbFromGFF warning meaning
GenomicFeatures
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 100
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2
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1.0k
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
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954
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
4.0 years ago Guandong Shang ▴ 40
0
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2
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797
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Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 40
2
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3
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1.7k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 4.1 years ago by 65k • written 4.1 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 4.1 years ago by 16k • written 4.1 years ago by ▴ 40
1
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2
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877
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.1 years ago by ★ 13k • written 4.1 years ago by ▴ 40
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0
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904
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 4.2 years ago by 3.8k • written 4.2 years ago by • 0
0
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2
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972
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biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
8
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12
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5.5k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 21 months ago by • 0 • written 9.1 years ago by ▴ 20
2
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3
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1.1k
views
GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 4.3 years ago by 65k • written 4.3 years ago by ▴ 30
0
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3
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932
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 4.3 years ago by ★ 11k • written 4.4 years ago by ▴ 90
0
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8
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1.6k
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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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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