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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
703
views
Conversion of RefSeq data to chromosomal position
RefSeq
Chromosome
Mutalyzer
4.8 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 8.5 years ago by
Hervé Pagès
16k • written 8.5 years ago by
Sebastien Vigneau
▴ 10
8
votes
7
replies
4.0k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 9.0 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: displaying the differential expression with deseq2 over 4X2 samples with the in
by
Martijn
• 0
thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…
Comment: plyranges: find exact GRanges match keeping metadata columns
by
alexis.weinreb
• 0
Thank you, this does clarify the available options.
Answer: displaying the differential expression with deseq2 over 4X2 samples with the in
by
James W. MacDonald
67k
If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq?
by
jodan
• 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Answer: Unused arguments error without used arguments in GSVA?
by
jodan
• 0
It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…
Votes
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
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