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refseq
•
reset
0
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606
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How can I translate NM_xxx.y:c.xxG>C mRNA sequences to corresponding NC_xxx.y:g.xxxC>G chromosomal coordinates?
refseq
Bioconductor
conversion
2.2 years ago
heiko_kin
▴ 50
0
votes
0
replies
261
views
Conversion of RefSeq data to chromosomal position
RefSeq
Chromosome
Mutalyzer
2.8 years ago
heiko_kin
▴ 50
0
votes
5
replies
940
views
Changing Gene ID annotation style - working with Salmon output [NM...] and resulting count files are numeric-only IDs
tximport
Gene IDs
txdb
RefSeq
Salmon
updated 3.0 years ago by
Michael Love
39k • written 3.0 years ago by
holmkn
• 0
1
vote
3
replies
2.1k
views
ENSEBL gene_ID in edgeR analysis
edgeR
ENEMBL
RefSeq
updated 3.9 years ago by
Gordon Smyth
47k • written 3.9 years ago by
mzillur
• 0
6
votes
7
replies
2.1k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures
maketxdbfromucsc
refseq
updated 6.5 years ago by
Hervé Pagès
16k • written 6.5 years ago by
Sebastien Vigneau
▴ 10
7
votes
7
replies
2.6k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 7.0 years ago by
Hervé Pagès
16k • written 7.0 years ago by
gokcen.eraslan
▴ 10
2
votes
2
replies
1.8k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 7.2 years ago by
Robert Castelo
★ 3.0k • written 7.2 years ago by
efoss
▴ 10
4
votes
1
reply
3.1k
views
getting the longest transcript by gene from Refseq
refseq
annotationhub
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
dalloliogm
▴ 40
2
votes
2
replies
1.2k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 7.6 years ago by
xiaojing.wang
▴ 50 • written 7.6 years ago by
kristenbeck527
• 0
9 results • Page
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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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