Showing : GenomicFeatures • reset
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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
2
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1
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385
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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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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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1.5k
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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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453
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Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
8 months ago Geert ▴ 10
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2
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906
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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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Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 10 months ago by 16k • written 11 months ago by • 0
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431
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Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
12 months ago Shreyash • 0
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8
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1.4k
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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
13 months ago davidhillis • 0
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2
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782
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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 16 months ago by 65k • written 16 months ago by • 0
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450
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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
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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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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
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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
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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
2.4 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 2.4 years ago by 16k • written 2.4 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
2.4 years ago Madza Farias-Virgens • 0
2
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2
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885
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Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 2.4 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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1000
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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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1.4k
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Is there anyway to replace seqlevels in a txdb
GenomicFeatures
2.7 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
2.7 years ago A.J. ▴ 20
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0
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811
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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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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
3.0 years ago António Miguel de Jesus Domingues ▴ 490
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5
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2.7k
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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
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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1.0k
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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
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698
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pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 3.2 years ago by ▴ 80 • written 3.5 years ago by ▴ 10
0
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1
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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
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7
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1.5k
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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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1.2k
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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
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6
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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
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1
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1.2k
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makeTxDbFromGFF warning meaning
GenomicFeatures
updated 3.9 years ago by 65k • written 3.9 years ago by ▴ 100
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2
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1.0k
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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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954
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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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797
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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
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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 4.1 years ago by ▴ 40
1
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2
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877
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 4.1 years ago by ★ 13k • written 4.1 years ago by ▴ 40
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0
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902
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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972
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biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
8
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12
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5.5k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 21 months ago by • 0 • written 9.1 years ago by ▴ 20
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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932
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 4.3 years ago by ★ 11k • written 4.4 years ago by ▴ 90
0
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8
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1.6k
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
50 results • Page 1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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