Showing : GenomicFeatures • reset
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Inconsistencies between accessor functions for TxDb databases with selected seqlevels.
TxDb GenomicFeatures GenomeInfoDb
1 day ago dbsgtk • 0
2
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3
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578
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Guitar R package requires update due to dependency GenomicFeatures
GenomicFeatures Guitar txdbmaker GenomicRanges
written 6 weeks ago by ▴ 10
4
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9
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3.3k
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Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 12 months ago by ★ 3.4k • written 14 months ago by ▴ 20
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3
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773
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How to get The evolutionary conservation scores for lncRNAs by the phastCons100way.UCSC.hg38 (3.7.1) R package
txdbmaker GenomicScores phastCons100way.UCSC.hg38 GenomicFeatures
15 months ago rania.alanany • 0
3
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3
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920
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
16 months ago • updated 14 months ago mat149 ▴ 80
0
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2
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1.2k
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Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
written 2.0 years ago by ▴ 10
2
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1
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1.6k
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Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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1
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1.4k
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How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
2.3 years ago rohitsatyam102 ▴ 20
2
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3
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5.5k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
2
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2
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1.3k
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Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
2.5 years ago Geert ▴ 10
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2
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2.1k
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What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
2.6 years ago gernophil • 0
1
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4
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1.4k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 2.7 years ago by 16k • written 2.7 years ago by • 0
1
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0
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1.0k
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Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
2.8 years ago Shreyash ▴ 10
4
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8
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3.4k
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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
2.9 years ago davidhillis • 0
0
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2
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1.6k
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how to match salmon output to txname
GenomicFeatures tximport salmon
written 3.1 years ago by • 0
0
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5
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2.1k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
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0
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947
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
3.3 years ago nattzy94 ▴ 20
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2
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1.9k
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How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 10
0
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4
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3.2k
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error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 3.7 years ago by 16k • written 3.7 years ago by • 0
5
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9
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2.7k
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Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.5 years ago by 43k • written 3.9 years ago by • 0
0
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18
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6.2k
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Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
4.0 years ago rbenel ▴ 50
3
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3
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2.2k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 3.8 years ago by 68k • written 4.1 years ago by ▴ 30
1
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2
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2.1k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
4.2 years ago Madza Farias-Virgens • 0
2
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3
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4.2k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 4.2 years ago by 16k • written 4.2 years ago by • 0
1
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2
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1.7k
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NAs in my txdb tx_name
GenomicFeatures Biostrings
4.2 years ago Madza Farias-Virgens • 0
2
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2
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1.4k
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 4.3 years ago by 16k • written 4.3 years ago by • 0
5
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2
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1.8k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.4 years ago Pratik Mehta ▴ 10
0
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1
reply
1.8k
views
install GenomicFeatures fail
GenomicFeatures install
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 80
1
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4
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2.3k
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Is there anyway to replace seqlevels in a txdb
GenomicFeatures
4.5 years ago A.J. ▴ 20
1
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3
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1.8k
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Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
4.5 years ago A.J. ▴ 20
1
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0
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1.7k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
4.6 years ago Matthias Munz ▴ 20
0
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0
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1.3k
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
4.8 years ago António Miguel de Jesus Domingues ▴ 510
0
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5
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3.9k
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
4.9 years ago sieminsk • 0
2
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2
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2.3k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
5.0 years ago erhoppe • 0
0
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6
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2.0k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
5.0 years ago rproendo ▴ 30
0
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3
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1.8k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 4.3 years ago by • 0 • written 5.3 years ago by ▴ 120
0
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2
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4.7k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
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1
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1.1k
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 5.0 years ago by ▴ 80 • written 5.3 years ago by ▴ 10
0
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1
reply
6.2k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 90
3
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7
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2.3k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 30
0
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1
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1.9k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 5.5 years ago by 4.3k • written 5.5 years ago by • 0
3
votes
6
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3.4k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 120
0
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1
reply
1.9k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 100
0
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2
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1.7k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 5.8 years ago by ★ 11k • written 5.8 years ago by ▴ 10
0
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0
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1.4k
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A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
5.8 years ago Guandong Shang ▴ 40
0
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2
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1.2k
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 40
2
votes
3
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2.5k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 100
3
votes
4
replies
1.7k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 5.9 years ago by 16k • written 5.9 years ago by ▴ 40
1
vote
2
replies
1.4k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 40
0
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0
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1.4k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 6.0 years ago by 4.3k • written 6.0 years ago by • 0
293 results • Page 1 of 6
Recent ...
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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Subsetting data verses contrasts [DESeq2]?
A: WGCNA differences two groups 10 replicates each group
A: WGCNA sample size minimum: why?
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
Answer: Can you colour dendrogram branch clusters in pheatmap?
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