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
4.4 years ago heiko_kin ▴ 60
0
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0
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759
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Conversion of RefSeq data to chromosomal position
RefSeq Chromosome Mutalyzer
5.0 years ago heiko_kin ▴ 60
0
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5
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2.5k
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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 5.2 years ago by 43k • written 5.2 years ago by • 0
1
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3
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3.3k
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ENSEBL gene_ID in edgeR analysis
edgeR ENEMBL RefSeq
updated 6.1 years ago by 52k • written 6.1 years ago by • 0
6
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7
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2.9k
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makeTxDbFromUCSC fails to download refLink table
genomicfeatures maketxdbfromucsc refseq
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 10
8
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7
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4.2k
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Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb
updated 9.3 years ago by 16k • written 9.3 years ago by ▴ 10
2
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2
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3.4k
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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 9.4 years ago by ★ 3.4k • written 9.4 years ago by ▴ 10
4
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1
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4.1k
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getting the longest transcript by gene from Refseq
refseq annotationhub
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 50
2
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2
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1.9k
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customProDB: issues getting dbSNP data for human (hg19)
customprodb dbsnp refseq varianttools
updated 9.8 years ago by ▴ 50 • written 9.8 years ago by • 0
9 results • Page 1 of 1
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Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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