Showing : RefSeq • reset
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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
5.1 years ago heiko_kin ▴ 60
0
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0
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945
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Conversion of RefSeq data to chromosomal position
RefSeq Chromosome Mutalyzer
5.8 years ago heiko_kin ▴ 60
0
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5
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2.9k
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 6.0 years ago by 43k • written 6.0 years ago by • 0
1
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3
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3.5k
views
ENSEBL gene_ID in edgeR analysis
edgeR ENEMBL RefSeq
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
6
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7
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3.2k
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makeTxDbFromUCSC fails to download refLink table
genomicfeatures maketxdbfromucsc refseq
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 10
8
votes
7
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4.8k
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Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 10
2
votes
2
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3.7k
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using the "promoters" function with an "OrganismDb" to generate "GRanges" with "REFSEQ" rather than UCSC gene names
promoter granges refseq ucsc organismdb
updated 10.1 years ago by ★ 3.4k • written 10.1 years ago by ▴ 10
4
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1
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4.3k
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getting the longest transcript by gene from Refseq
refseq annotationhub
updated 10.3 years ago by 25k • written 10.3 years ago by ▴ 50
2
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2
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2.1k
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customProDB: issues getting dbSNP data for human (hg19)
customprodb dbsnp refseq varianttools
updated 10.5 years ago by ▴ 50 • written 10.5 years ago by • 0
9 results • Page 1 of 1
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Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Votes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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