Showing : GenomicFeatures • reset
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Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 11 weeks ago by 65k • written 11 weeks ago by ▴ 10
2
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1
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396
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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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454
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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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1.6k
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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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458
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Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
9 months ago • updated 8 months ago Geert ▴ 10
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2
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927
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What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
10 months ago gernophil • 0
1
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4
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742
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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 11 months ago by 16k • written 11 months ago by • 0
1
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0
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457
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Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
12 months ago Shreyash ▴ 10
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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796
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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 17 months ago by 65k • written 17 months ago by • 0
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460
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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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1.6k
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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 2.4 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
2.5 years ago • updated 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 2.5 years ago by 16k • written 2.5 years ago by • 0
1
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2
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1.0k
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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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892
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Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 2.5 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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1.0k
views
install GenomicFeatures fail
GenomicFeatures install
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 80
1
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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
1
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3
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1.1k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
2.7 years ago A.J. ▴ 20
0
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0
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820
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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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802
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.0 years ago António Miguel de Jesus Domingues ▴ 510
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5
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2.8k
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.1 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
3.2 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
0
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1
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702
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.2 years ago by ▴ 80 • written 3.6 years ago by ▴ 10
0
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1
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4.5k
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
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1.2k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 3.8 years ago by 3.8k • 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 3.8 years ago by 25k • written 3.8 years ago by ▴ 120
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1
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1.2k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 3.9 years ago by 65k • written 3.9 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 4.0 years ago by ★ 11k • written 4.0 years ago by ▴ 10
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0
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960
views
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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803
views
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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891
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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914
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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982
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biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
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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939
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
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8
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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
2
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0
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791
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SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
4.5 years ago rmash ▴ 20
50 results • Page 1 of 1
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
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Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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