User: deepak18

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deepak1810
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Posts by deepak18

<prev • 19 results • page 2 of 2 • next >
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DEXSeq Installation Error
... I am trying to install DEXSeq on R version 3.6.1 but I am getting the following error: ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’. * removing ‘/home/erpl/R/x86_64-pc-linux-gnu-library/3.6/geneplotter’ ERROR: dependency ‘annotate’ is not available for p ...
dexseq rna-seq alternative splicing written 11 months ago by deepak1810 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: Aligning multiple Fastq files using Bowtie2
... Thank you for your valuable reply. ...
written 11 months ago by deepak1810
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Comment: C: Aligning multiple Fastq files using Bowtie2
... Also if it is possible then how can I get multiple SAM output files each corresponding to one sample. ...
written 11 months ago by deepak1810
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Aligning multiple Fastq files using Bowtie2
... I want to align multiple paired end Fastq files belonging to different samples (RNA-seq reads) using Bowtie2. Bowtie allows alignment for multiple Fastq files at once but produces only one output SAM file specified by -S flag. I wanted to know whether this output file would be useful for downstream ...
bowtie2 fastq alignment rna-seq written 11 months ago by deepak1810 • updated 11 months ago by WouterDeCoster44k
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Isoform level TCGA RNA-seq Expression data
... I have Isoform level RNA-seq data from The Cancer Genome Atlas and I want to check the difference the difference in the level of a particular isoform between cancer and normal samples. Is there any software or R package which I can use to plot a boxplot showing difference in that isoform between nor ...
R isoform_expression rna-seq tcga linux written 12 months ago by deepak1810 • updated 12 months ago by igor11k
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Hypothesis testing for isoform level TCGA RNA-seq expression data
... I am working with isoform-level RNA-seq data from TCGA. After calculating isoform fraction (expression level of a particular isoform divided by the total expression of all the isoforms belonging to a gene) for all isoforms in cancer and tumor samples I wanted to check if the expression of a particul ...
R next-gen rna-seq tcga written 12 months ago by deepak1810 • updated 12 months ago by Biostar ♦♦ 20
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Comment: C: Gene Set Enrichment Analysis with RNA-seq data
... Thank you for the comments. I was able to perform GSEA using the software successfully without any pre-processing. ...
written 13 months ago by deepak1810
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Comment: C: Gene Set Enrichment Analysis with RNA-seq data
... Actually I am facing problems with both. For analysis of RNA-seq data with the software we need to filter out low count measurements. What cut off should I put for this filter step and do I need to do some more pre-processing before I can go with the analysis? ...
written 13 months ago by deepak1810
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Gene Set Enrichment Analysis with RNA-seq data
... I have TCGA data for RNA expression for breast cancer samples (log2 normalised fpkm values) and I want to perform GSEA on it to look which gene sets are enriched in cancer samples vs normal samples. Which is the best platform to perform GSEA with RNA-seq software? Which will better, the software by ...
R next-gen rna-seq written 13 months ago by deepak1810

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