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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
504
views
Conversion of RefSeq data to chromosomal position
RefSeq
Chromosome
Mutalyzer
4.0 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 4.2 years ago by
Michael Love
41k • written 4.2 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
2.5k
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
3.4k
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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Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error
by
James W. MacDonald
65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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