Showing : GenomicFeatures • reset
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Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 3 months ago by 65k • written 3 months ago by ▴ 10
2
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1
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424
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Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 5 months ago by 65k • written 5 months ago by • 0
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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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1.7k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 8 months ago by 50k • written 8 months ago by • 0
2
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2
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475
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Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
9 months ago Geert ▴ 10
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2
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967
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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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764
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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
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473
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Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
13 months ago • updated 12 months ago Shreyash ▴ 10
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8
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1.5k
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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
14 months ago davidhillis • 0
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2
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816
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how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 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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469
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Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
19 months ago nattzy94 ▴ 20
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2
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How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 20 months ago by 42k • written 20 months ago by ▴ 10
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4
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2.1k
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error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 24 months ago by 16k • written 24 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 42k • written 2.1 years ago by • 0
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18
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3.6k
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Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
2.3 years ago • updated 2.2 years ago rbenel ▴ 40
3
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3
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1.5k
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GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 2.0 years ago by 65k • written 2.4 years ago by ▴ 30
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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 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
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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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901
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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
2.7 years ago Pratik Mehta ▴ 10
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1
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1.0k
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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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1.5k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
2.8 years ago A.J. ▴ 20
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3
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1.1k
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Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
2.8 years ago A.J. ▴ 20
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0
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839
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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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814
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.1 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
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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
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6
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1.2k
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Splitting TxDb by Strand
GenomicFeatures TxDb
3.3 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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Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 3.5 years ago by 42k • written 3.5 years ago by • 0
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1
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710
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.3 years ago by ▴ 80 • written 3.6 years ago by ▴ 10
0
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1
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4.5k
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Add gene symbol when making TxDb
txdb genomicfeatures
updated 3.7 years ago by 65k • written 3.8 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 3.8 years ago by 65k • written 3.8 years ago by ▴ 30
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1
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1.2k
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error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 3.8 years ago by 3.9k • written 3.8 years ago by • 0
3
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6
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2.0k
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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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1.2k
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makeTxDbFromGFF warning meaning
GenomicFeatures
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 100
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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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974
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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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813
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Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.1 years ago by 65k • written 4.1 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
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how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 4.1 years ago by 16k • written 4.2 years ago by ▴ 40
1
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2
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900
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Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.2 years ago by ★ 13k • written 4.2 years ago by ▴ 40
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0
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932
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Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 4.2 years ago by 3.9k • written 4.2 years ago by • 0
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2
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990
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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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946
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Resize exons in transcript to total width
genomicranges genomicfeatures
updated 4.4 years ago by ★ 11k • written 4.4 years ago by ▴ 90
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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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802
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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
Recent ...
Replies
Comment: error running enricher from clusterprofiler by Yael • 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Votes
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
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