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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
4.2 years ago
heiko_kin
▴ 60
0
votes
0
replies
716
views
Conversion of RefSeq data to chromosomal position
RefSeq
Chromosome
Mutalyzer
4.9 years ago
heiko_kin
▴ 60
0
votes
5
replies
2.4k
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 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
holmkn
• 0
1
vote
3
replies
3.2k
views
ENSEBL gene_ID in edgeR analysis
edgeR
ENEMBL
RefSeq
updated 5.9 years ago by
Gordon Smyth
52k • written 5.9 years ago by
mzillur
• 0
6
votes
7
replies
2.8k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures
maketxdbfromucsc
refseq
updated 8.6 years ago by
Hervé Pagès
16k • written 8.6 years ago by
Sebastien Vigneau
▴ 10
8
votes
7
replies
4.1k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 9.1 years ago by
Hervé Pagès
16k • written 9.1 years ago by
gokcen.eraslan
▴ 10
2
votes
2
replies
3.2k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 9.2 years ago by
Robert Castelo
★ 3.4k • written 9.2 years ago by
efoss
▴ 10
4
votes
1
reply
4.0k
views
getting the longest transcript by gene from Refseq
refseq
annotationhub
updated 9.4 years ago by
Martin Morgan
25k • written 9.4 years ago by
dalloliogm
▴ 50
2
votes
2
replies
1.9k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 9.6 years ago by
xiaojing.wang
▴ 50 • written 9.6 years ago by
kristenbeck527
• 0
9 results • Page
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Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.6k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Comment: MEDIPS - error using MEDIPS.CpGenrich
by
sg
• 0
I have the same error when I use 22 chrs with the paramenters chr.select: Error in h(simpleError(msg, call)) : error in evaluating the …
Comment: Overcoming confounding in batch effect correction
by
mimi
• 0
https://www.bioconductor.org/packages/release/BiocViews.html#___BiologicalQuestion
Comment: GSVA on RNAseq data
by
Robert Castelo
★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Answer: Store Matrix in DataFrame Cell
by
James W. MacDonald
68k
Put it in a list and put the list in a column.
Votes
Overcoming confounding in batch effect correction
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
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