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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
3.3 years ago
heiko_kin
▴ 60
0
votes
0
replies
488
views
Conversion of RefSeq data to chromosomal position
RefSeq
Chromosome
Mutalyzer
4.0 years ago
heiko_kin
▴ 60
0
votes
5
replies
1.8k
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 4.2 years ago by
Michael Love
41k • written 4.2 years ago by
holmkn
• 0
1
vote
3
replies
2.7k
views
ENSEBL gene_ID in edgeR analysis
edgeR
ENEMBL
RefSeq
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
mzillur
• 0
6
votes
7
replies
2.5k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures
maketxdbfromucsc
refseq
updated 7.7 years ago by
Hervé Pagès
16k • written 7.7 years ago by
Sebastien Vigneau
▴ 10
8
votes
7
replies
3.4k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 8.2 years ago by
Hervé Pagès
16k • written 8.2 years ago by
gokcen.eraslan
▴ 10
2
votes
2
replies
2.5k
views
using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter
granges
refseq
ucsc
organismdb
updated 8.3 years ago by
Robert Castelo
★ 3.1k • written 8.3 years ago by
efoss
▴ 10
4
votes
1
reply
3.7k
views
getting the longest transcript by gene from Refseq
refseq
annotationhub
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 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 8.7 years ago by
xiaojing.wang
▴ 50 • written 8.7 years ago by
kristenbeck527
• 0
9 results • Page
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
Answer: Microarray Limma Model fitting and DEG
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