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RefSeq
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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
3.4 years ago
heiko_kin
▴ 60
0
votes
0
replies
515
views
Conversion of RefSeq data to chromosomal position
RefSeq
Chromosome
Mutalyzer
4.1 years ago
heiko_kin
▴ 60
0
votes
5
replies
1.9k
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 4.3 years ago by
Michael Love
42k • written 4.3 years ago by
holmkn
• 0
1
vote
3
replies
2.8k
views
ENSEBL gene_ID in edgeR analysis
edgeR
ENEMBL
RefSeq
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
mzillur
• 0
6
votes
7
replies
2.6k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures
maketxdbfromucsc
refseq
updated 7.8 years ago by
Hervé Pagès
16k • written 7.8 years ago by
Sebastien Vigneau
▴ 10
8
votes
7
replies
3.5k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 8.3 years ago by
Hervé Pagès
16k • written 8.3 years ago by
gokcen.eraslan
▴ 10
2
votes
2
replies
2.6k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 8.5 years ago by
Robert Castelo
★ 3.3k • written 8.5 years ago by
efoss
▴ 10
4
votes
1
reply
3.7k
views
getting the longest transcript by gene from Refseq
refseq
annotationhub
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
dalloliogm
▴ 50
2
votes
2
replies
1.7k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 8.8 years ago by
xiaojing.wang
▴ 50 • written 8.8 years ago by
kristenbeck527
• 0
9 results • Page
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Replies
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(fit2, vector_group, probe_annotation, contrasts = contrast_matrix, gs.annots = gs.…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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Gyan Prakash Mishra
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50k
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WouterDeCoster
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Michael Love
42k
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Malcolm Cook
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