Showing : GenomicFeatures • reset
4
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9
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2.3k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 9 weeks ago by ★ 3.4k • written 3 months ago by ▴ 20
0
votes
3
replies
403
views
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
4 months ago rania.alanany • 0
3
votes
3
replies
549
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
6 months ago • updated 3 months ago mat149 ▴ 80
0
votes
1
reply
691
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 13 months ago by 68k • written 13 months ago by ▴ 10
2
votes
1
reply
1.1k
views
Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
1
reply
980
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
17 months ago rohitsatyam102 ▴ 20
2
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3
replies
4.1k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 18 months ago by 52k • written 18 months ago by • 0
2
votes
2
replies
849
views
Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
20 months ago Geert ▴ 10
0
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2
replies
1.6k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
21 months ago gernophil • 0
1
vote
4
replies
1.1k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 22 months ago by 16k • written 22 months ago by • 0
1
vote
0
replies
759
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
23 months ago Shreyash ▴ 10
4
votes
8
replies
2.4k
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
2.0 years ago davidhillis • 0
0
votes
2
replies
1.3k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.2 years ago by • 0
0
votes
5
replies
1.7k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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0
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683
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
2.5 years ago nattzy94 ▴ 20
0
votes
2
replies
1.5k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 10
0
votes
4
replies
2.8k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 2.9 years ago by 16k • written 2.9 years ago by • 0
5
votes
9
replies
2.1k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 2.7 years ago by 43k • written 3.0 years ago by • 0
0
votes
18
replies
4.9k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
3.2 years ago • updated 3.1 years ago rbenel ▴ 40
3
votes
3
replies
1.9k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 2.9 years ago by 68k • written 3.3 years ago by ▴ 30
1
vote
2
replies
1.7k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.4 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.4k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.4 years ago by 16k • written 3.4 years ago by • 0
1
vote
2
replies
1.4k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.4 years ago Madza Farias-Virgens • 0
2
votes
2
replies
1.2k
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 3.4 years ago by 16k • written 3.4 years ago by • 0
5
votes
2
replies
1.4k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.6 years ago Pratik Mehta ▴ 10
0
votes
1
reply
1.6k
views
install GenomicFeatures fail
GenomicFeatures install
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 80
1
vote
4
replies
2.0k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
3.7 years ago A.J. ▴ 20
1
vote
3
replies
1.5k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
3.7 years ago A.J. ▴ 20
1
vote
0
replies
1.4k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.7 years ago Matthias Munz ▴ 20
0
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0
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1.1k
views
annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.9 years ago António Miguel de Jesus Domingues ▴ 510
0
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5
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3.5k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
4.0 years ago sieminsk • 0
2
votes
2
replies
2.1k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
4.1 years ago erhoppe • 0
0
votes
6
replies
1.6k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
4.2 years ago rproendo ▴ 30
0
votes
3
replies
1.5k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 3.4 years ago by • 0 • written 4.4 years ago by ▴ 120
0
votes
2
replies
3.9k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
1
reply
886
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 4.1 years ago by ▴ 80 • written 4.5 years ago by ▴ 10
0
votes
1
reply
5.6k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 4.6 years ago by 68k • written 4.6 years ago by ▴ 90
3
votes
7
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1.9k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 30
0
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1
reply
1.6k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 4.7 years ago by 4.1k • written 4.7 years ago by • 0
3
votes
6
replies
2.7k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 4.7 years ago by 25k • written 4.7 years ago by ▴ 120
0
votes
1
reply
1.6k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 100
0
votes
2
replies
1.3k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.9 years ago by ★ 11k • written 4.9 years ago by ▴ 10
0
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0
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1.2k
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
4.9 years ago Guandong Shang ▴ 40
0
votes
2
replies
1.1k
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 40
2
votes
3
replies
2.2k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 100
3
votes
4
replies
1.4k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 5.0 years ago by 16k • written 5.0 years ago by ▴ 40
1
vote
2
replies
1.2k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 5.1 years ago by ★ 13k • written 5.1 years ago by ▴ 40
0
votes
0
replies
1.2k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 5.1 years ago by 4.1k • written 5.1 years ago by • 0
0
votes
2
replies
1.2k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
8
votes
12
replies
6.4k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.7 years ago by • 0 • written 10.0 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: compute_fasta_digest does not match Salmon index hash by Michael Love 43k
Can you provide more details on when this is happening? The salmon index is the definitive hash associated with the quant files, so I'm con…
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
Oh wait. You want to map from Ensembl to NCBI? That's hard to do with model organisms, let alone non-model. This `OrgDb` doesn't have Ensem…
Answer: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
You can use the `AnnotationHub` ``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% sna…
Answer: List of Deprecated Packages for Bioc3.20 by shepherl 4.1k
HTqPCR has been fixed and will be re-instated in 3.21
Comment: Question about using LRT test for time course experiments with DESeq2 by Rob • 0
Just to pick up on this thread as its really helpful for understanding the LRT test. The LRT test is given any genes that change within the…
Votes
what the test method for enrichGO in clusterProfiler?
A: single-cells RNA-seq analysis by MAST with unbalanced group size
Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
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