Showing : genomicfeatures • reset
0
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217
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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
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 3 months ago by ▴ 10 • written 8.4 years ago by ▴ 10
2
votes
1
reply
388
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 4 months ago by 65k • written 4 months ago by • 0
0
votes
1
reply
447
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
6 months ago rohitsatyam102 ▴ 20
2
votes
3
replies
1.6k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
2
votes
2
replies
455
views
Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
8 months ago Geert ▴ 10
0
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2
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915
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
10 months ago gernophil • 0
1
vote
4
replies
735
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 11 months ago by 16k • written 11 months ago by • 0
0
votes
0
replies
437
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
12 months ago Shreyash • 0
4
votes
8
replies
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
0
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2
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788
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 15 months ago by • 0
0
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5
replies
1.2k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 16 months ago by 65k • written 16 months ago by • 0
0
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0
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455
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
18 months ago nattzy94 ▴ 20
0
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2
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1.0k
views
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
5
votes
9
replies
1.6k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 21 months ago by 41k • written 2.1 years ago by • 0
4
votes
3
replies
1.9k
views
How to extract only mRNA from TxDb object?
genomicfeatures
updated 21 months ago by ▴ 40 • written 7.5 years ago by ▴ 50
8
votes
12
replies
5.5k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 21 months ago by • 0 • written 9.1 years ago by ▴ 20
0
votes
4
replies
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
6
votes
5
replies
4.7k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 24 months ago by 16k • written 5.2 years ago by • 0
3
votes
3
replies
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
0
votes
18
replies
3.5k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.2 years ago rbenel ▴ 40
0
votes
1
reply
1.3k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 2.4 years ago by • 0 • written 8.4 years ago by ▴ 10
1
vote
2
replies
1.2k
views
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
votes
3
replies
2.5k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
1
vote
2
replies
1.0k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
2.4 years ago Madza Farias-Virgens • 0
2
votes
2
replies
889
views
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
0
votes
3
replies
1.1k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 2.5 years ago by • 0 • written 3.5 years ago by ▴ 120
5
votes
2
replies
1.1k
views
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
0
votes
1
reply
1.0k
views
install GenomicFeatures fail
GenomicFeatures install
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 80
1
vote
4
replies
1.4k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
2.7 years ago A.J. ▴ 20
1
vote
3
replies
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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815
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.8 years ago Matthias Munz ▴ 10
0
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0
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797
views
annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.0 years ago António Miguel de Jesus Domingues ▴ 490
0
votes
5
replies
2.7k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
3.1 years ago sieminsk • 0
2
votes
2
replies
1.7k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
3.2 years ago erhoppe • 0
5
votes
5
replies
1.9k
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 3.2 years ago by ★ 1.5k • written 4.7 years ago by ▴ 10
0
votes
1
reply
700
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.2 years ago by ▴ 80 • written 3.5 years ago by ▴ 10
0
votes
6
replies
1.2k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
3.2 years ago rproendo ▴ 20
0
votes
2
replies
3.1k
views
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
votes
1
reply
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
votes
7
replies
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
0
votes
1
reply
1.2k
views
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
votes
6
replies
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
votes
1
reply
1.2k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 100
0
votes
2
replies
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
0
votes
0
replies
958
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
votes
2
replies
799
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 40
2
votes
3
replies
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
votes
4
replies
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
vote
2
replies
884
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.2 years ago by ★ 13k • written 4.2 years ago by ▴ 40
50 results • Page 1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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