User: Lila M

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Lila M 770
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Posts by Lila M

<prev • 313 results • page 1 of 32 • next >
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how to plot an abundance table with ssp from metagenominc data
... Hi all, I need to analyze some metagenomic data from microbiome in human in two conditions: antibiotics and non antibiotics. I have two data set, one abundance table and one ID table (with ID and treatment: antibiotic/non antibiotic). #abundance table: df name ssp1 ssp2 ...
microbiome otus metagenomic written 4 hours ago by Lila M 770
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Comment: C: How to do FPKM differential analysis?
... In most published articles and studies is hardly recommended to use normalized counts rather than fpkm for DE analysis. You do not agree with that? ...
written 2 days ago by Lila M 770
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Comment: C: How to do FPKM differential analysis?
... Hi, I do not recommend to use `FPKM` for DE analysis. Is better to use the normalized counts (vst/vsd) generated by `DESeq2`. (For more info have a look in [here][1]). However, there is a function in DESeq2 called `fpkm()` that allow you to do that [1]: https://bioconductor.org/packages/3.7/bi ...
written 3 days ago by Lila M 770
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Comment: C: Differential network analysis for two treatments
... You can use `DESeq2` for differential expression analysis (see in [here][1] ) and plot the top 100 or 500 more expressed genes. As an example: library(DESeq2) dds <- DESeqDataSetFromMatrix( countData = count.table, colData = samples, design = ~ status) dds2 <- D ...
written 3 days ago by Lila M 770
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Answer: A: Annotate .bed file with gene names and exon
... Hope this help library(biomaRt) mart <- useDataset("mmusculus_gene_ensembl", useMart("ensembl")) annotated <- getBM(filters= "yourfilter", attributes= c("chromosome_name", "exon_chrom_start", "exon_chrom_end", "strand", "ensembl_gene_id","ensembl_exon_id"), values ...
written 4 days ago by Lila M 770
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Comment: C: Column that include Enterez ID converted from wheat Ensemble ID using biomart pa
... I guess that, so use the function `listAttributes` and find `entrezgene` (copy and paste to your code). However, as @Kevin suggest, is possible that not annotation exist at all for your genes. ...
written 7 days ago by Lila M 770
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Comment: C: Column that include Enterez ID converted from wheat Ensemble ID using biomart pa
... The column has been created but is empty? Or is there not column at all? Try first with `entrezgene` only and see if any error or warning message appears. ...
written 7 days ago by Lila M 770
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Comment: C: RNA-Seq: Getting Started with Kallisto
... If it helps..up vote the answer! ...
written 7 days ago by Lila M 770
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Comment: C: How to use htseq-count with several samples ?
... You have to run it separately for each sample. One you get the counts you can use R to create a unique matrix as res <- mclapply(dir(pattern="*.counts", full.names=TRUE), function(fil){ read.delim(fil, header=FALSE, stringsAsFactors=FALSE) }, ...
written 7 days ago by Lila M 770
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Comment: C: where to download methylation data for colorectal cancer?
... Thank you, and how can I downloaded them at once? there is any fast query? Thank you ...
written 8 days ago by Lila M 770

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Commentator 7 days ago, created a comment with at least 3 up-votes. For C: error while reading bigwig files in computeMatrix (deeptools)
Commentator 7 days ago, created a comment with at least 3 up-votes. For C: error while reading bigwig files in computeMatrix (deeptools)
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Great Question 8 months ago, created a question with more than 5,000 views. For How to convert bedgraph to bigwig?
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Popular Question 10 months ago, created a question with more than 1,000 views. For How to convert bedgraph to bigwig?

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