User: seeker

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seeker0
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Posts by seeker

<prev • 24 results • page 1 of 3 • next >
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how to create cnTable in maftools ?
... Hi , In the documentation "cnTable Custom copynumber data if gistic results are not available. Input file should a tab seperated three column table containing gene name, Sample name and copy number status". How should i create a cnTable if there is Amplification/Deletion for a particular gene in m ...
maftools written 9 weeks ago by seeker0 • updated 7 weeks ago by anand_mt40
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Comment: C: How to find the distance between the integration site and gene
... Michael, could you please explain this ...
written 5 months ago by seeker0
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Comment: C: How to find the distance between the integration site and gene
... tried distanceToNearest, but it does not gives the orientation of the position. For eg if it is  upstream or downstream apart from the gene. ...
written 5 months ago by seeker0
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How to find the distance between the integration site and gene
... Hello, I am trying to annotate my integration file with the nearest gene names and distance to the nearest gene (upstream and downstream) using hiAnnotator [nearestGenes <- getNearestFeature(alldata.rd, genes.rd ,"NearestGene")]. In the annotation file i could get the the nearest gene name and ...
genomicranges hiannotator written 5 months ago by seeker0 • updated 5 months ago by Michael Lawrence9.2k
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how to annotate TCGA snp6 data in gene centric approach
... How can i annotate SNP6 probe id with each gene separately  con = pd.genomewidesnp.6@getdb()  dbGetQuery(con, "select * from featureSet limit 906600") this gives an individual SNPs with its associated genes.    ...
microarray annotation dbgetquery pd.genomewidesnp.6 written 7 months ago by seeker0
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how to annotate TCGA snp6 data with genomic coordinates
... I want to annotate the SNP6 data from tcga with its chromosomal coordinates and allele information using bioconductor packages. Composite Element REF   Call    Confidence SNP_A-2131660   2       0.0048 SNP_A-1967418   2       0.1260 SNP_A-1969580   2       0.0047 SNP_A-4263484   1       0.0002 ...
microarray annotation tcga snp6.0 written 7 months ago by seeker0
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Comment: C: How to find the differentially expressed genes for paired tumor normal samples w
... The reason why i was worried about my design is because, if i look at the normalized read count  (rld) of tumor/control in Fgfr1 gene, there is average fold change on 1.5. Sample_1_Cont    Sample_1_Tum    Sample_2_Cont    Sample_2_Tumor    Sample_3_Cont    Sample_3_Tumor    Sample_4_Cont    Sample_ ...
written 18 months ago by seeker0
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Comment: C: How to find the differentially expressed genes for paired tumor normal samples w
... Please find the code below sample2 <- read.table("read.count.txt", sep = "/t", stringsAsFactors= F, header=T) sample2 <- sample2[!duplicated(sample2$Gene),] comSamples <- sample2[,-1] rownames(comSamples) <- sample2[,1] sample_1 <- colnames(comSamples) my_conditions <-  factor ...
written 18 months ago by seeker0
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Comment: C: How to find the differentially expressed genes for paired tumor normal samples w
... Michael, But when i tried  mcols(res, use.name = T), im getting  DataFrame with 6 rows and 2 columns                        type                                description                 <character>                                <character> baseMean   intermediate  mean of normalized ...
written 18 months ago by seeker0
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Comment: C: How to find the differentially expressed genes for paired tumor normal samples w
... Michael, But when i tried  mcols(res, use.name = T), im getting  DataFrame with 6 rows and 2 columns                        type                                description                 <character>                                <character> baseMean   intermediate  mean of normalized ...
written 18 months ago by seeker0

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Popular Question 15 months ago, created a question with more than 1,000 views. For DESeq2 installation error

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