Showing : genomicfeatures • reset
4
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9
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Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 7 weeks ago by ★ 3.4k • written 12 weeks ago by ▴ 20
3
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3
replies
525
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
5 months ago • updated 12 weeks ago mat149 ▴ 80
0
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3
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388
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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
4 months ago • updated 3 months ago rania.alanany • 0
0
votes
1
reply
676
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
4
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5
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3.7k
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How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 13 months ago by ▴ 10 • written 9.3 years 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
955
views
How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
16 months ago rohitsatyam102 ▴ 20
2
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3
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4.0k
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
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825
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Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
19 months ago Geert ▴ 10
0
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2
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1.6k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
20 months ago gernophil • 0
1
vote
4
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1.1k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 21 months ago by 16k • written 22 months ago by • 0
1
vote
0
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744
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
23 months ago Shreyash ▴ 10
4
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8
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2.3k
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 • updated 24 months ago davidhillis • 0
0
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2
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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
votes
0
replies
676
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
2.4 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
5
votes
9
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2.1k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 2.6 years ago by 43k • written 2.9 years ago by • 0
4
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3
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2.3k
views
How to extract only mRNA from TxDb object?
genomicfeatures
updated 2.6 years ago by ▴ 40 • written 8.4 years ago by ▴ 50
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
0
votes
4
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2.7k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 2.8 years ago by 16k • written 2.8 years ago by • 0
6
votes
5
replies
6.2k
views
Using GenomicFeatures to extract the upstream and downstream region of a transcript
genomicfeatures
updated 2.9 years ago by 16k • written 6.1 years ago by • 0
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 3.2 years ago by ▴ 30
0
votes
18
replies
4.8k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
3.1 years ago • updated 3.0 years ago rbenel ▴ 40
0
votes
1
reply
1.6k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 3.3 years ago by • 0 • written 9.3 years ago by ▴ 10
1
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2
replies
1.7k
views
How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
3.3 years ago Madza Farias-Virgens • 0
2
votes
3
replies
3.4k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 3.3 years ago by 16k • written 3.3 years ago by • 0
1
vote
2
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1.4k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
3.3 years ago Madza Farias-Virgens • 0
2
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2
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1.2k
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 3.3 years ago by 16k • written 3.4 years ago by • 0
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
5
votes
2
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1.4k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.5 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
1.9k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
3.6 years ago A.J. ▴ 20
1
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3
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1.5k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
3.6 years ago A.J. ▴ 20
1
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0
replies
1.4k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.6 years ago Matthias Munz ▴ 20
0
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0
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1.0k
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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
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Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
4.0 years ago sieminsk • 0
2
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2
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2.1k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
4.1 years ago erhoppe • 0
5
votes
5
replies
2.5k
views
threeUTRsByTranscript per GENE
GenomicFeatures Transcript gene threeUTRsByTranscript
updated 4.1 years ago by ★ 1.6k • written 5.6 years ago by ▴ 10
0
votes
1
reply
881
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 4.1 years ago by ▴ 80 • written 4.4 years ago by ▴ 10
0
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6
replies
1.6k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
4.1 years ago rproendo ▴ 30
0
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2
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3.8k
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
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1
reply
5.5k
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 4.6 years ago by 68k • written 4.6 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 4.6 years ago by 4.1k • written 4.6 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 4.8 years ago by 68k • written 4.8 years ago by ▴ 100
0
votes
2
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1.3k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 4.8 years ago by ★ 11k • written 4.8 years ago by ▴ 10
0
votes
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
1.0k
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 40
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Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data by silickas • 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
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Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
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