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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
41k • 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 8.4 years ago by
Robert Castelo
★ 3.3k • written 8.4 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
1.6k
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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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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