Showing : exons • reset
6
votes
4
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1.5k
views
the coordinates of exons of RefSeq or ENSEMBL genes
txdb genome exons
updated 3.5 years ago by 25k • written 3.5 years ago by ▴ 660
2
votes
4
replies
887
views
Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.knownGene: incorrect number of exons and overlapping exons
txdb txdb.hsapiens.ucsc.hg19.knowngene granges exons ucsc
updated 4.1 years ago by 62k • written 4.1 years ago by ▴ 10
0
votes
0
replies
429
views
Filtering probesets for HuEx ST1.0 after probeset normalization
microarray exons probefiltering
4.2 years ago GENOMIC_region • 0
2
votes
3
replies
650
views
Human Exon: arome.affymetrix residuals Inf value
exons exon array analysis
updated 4.3 years ago by 62k • written 4.3 years ago by • 0
2
votes
1
reply
1.2k
views
Extracting UTRs from exon and CDS data
genomeintervals UTRs exons CDS GenomicRanges
updated 5.5 years ago by 11k • written 5.5 years ago by ▴ 110
0
votes
3
replies
921
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Increased number of total exons in DEXSeq
dexseq exons grch37
5.9 years ago aditi ▴ 20
2
votes
6
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1.6k
views
Using TCGAbiolinks for exon and oligonucleotide level microarray
tcga tcgabiolinks microarray exons oligonucleotide
updated 6.7 years ago by ▴ 220 • written 6.7 years ago by • 0
3
votes
7
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1.0k
views
To find Differential expressed exons using xps package
xps exons
updated 6.9 years ago by ★ 3.9k • written 6.9 years ago by ▴ 110
0
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0
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900
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plotSplice plotting only exons passing the filter makes the plot loose gene structure
limma diffSplice plotSplice exons annotation
7.5 years ago Jose M Garcia Manteiga ▴ 310
0
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1
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1.6k
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Difference in TxDb.Hsapiens.UCSC.hg19.knownGene and UCSC knownGene
annotate exons txdb.hsapiens.ucsc.hg19.knowngene
7.6 years ago adnan.niazi • 0
0
votes
1
reply
959
views
Extract exon features from overlapping genes
GenomicFeatures exons
updated 7.7 years ago by 16k • written 7.7 years ago by • 0
11 results • Page 1 of 1
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Answer: struggling to create a heatmap by ATpoint ★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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