User: Javad

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Javad0
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Posts by Javad

<prev • 27 results • page 1 of 3 • next >
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Comment: C: single cell RNA-seq 10X genomics
... This paper is a good start to understand differences between single cell rna seq and bulk rna seq analysis. Stegle, Oliver, Sarah A. Teichmann, and John C. Marioni. "Computational and analytical challenges in single-cell transcriptomics." Nature Reviews Genetics 16.3 (2015): 133-145. ...
written 13 days ago by Javad0
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How to import read count matrix into CellDataSet object
... Dear all, I get stuck with something basic. I have a read count table (a matrix) and I want to import it into [monocle][1]. What is the format of feature data and pheno data that I need to use and what is the format of data matrix ? Thanks a lot [1]: http://cole-trapnell-lab.github.io/monocle- ...
rna-seq written 17 days ago by Javad0 • updated 17 days ago by Pierre Lindenbaum101k
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Comment: C: How I can produce graphs like this
... It is just a gene expression. I need to show the percentage of each gene in diffrerent group. each colour here represents a gene and the height of column represents the percentage of gene expression. ...
written 29 days ago by Javad0
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How I can produce graphs like this
... Hello every body, Could you please tell me which R package can I use to produce graphs like this? Thanks in advance. ![enter image description here][1] https://ibb.co/fTZMAm [1]: https://image.ibb.co/cW6CGR/Screenshot_from_2017_10_26_14_09_23.png ...
next-gen rna-seq written 29 days ago by Javad0 • updated 29 days ago by Sreeraj Thamban80
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Comment: C: How to run a Perl script
... Thanks, But how I can define the input and output file? ...
written 6 weeks ago by Javad0
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How to run a Perl script
... Hello, I do not have any experience in Perl scripting. I have a Perl script that is specifically designed to convert GFF/GTF formatted files to BED files ([here is the script][1]). Can any help me to run this script for format conversion. It would be grate if I can have a step by step guide about h ...
genome next-gen rna-seq written 6 weeks ago by Javad0 • updated 6 weeks ago by Samarth Kulshrestha100
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Comment: C: looking for an R package for GO term analysis
... Thank you very much for your response. Because I am new to this area, I would like to know a little bit about how GO term analysis works. There are few publications available but most of them are highly technical and hard to understand. Is there a good paper about it that explains the idea behind GO ...
written 6 weeks ago by Javad0
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looking for an R package for GO term analysis
... Hello, Can anyone suggest a simple R package to perform GO term analysis. Specially I am looking for a package that can produces publication quality figures and heatmaps regarding GO term results. Thanks in advance ...
next-gen rna-seq written 6 weeks ago by Javad0 • updated 6 weeks ago by Kevin Blighe7.3k
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Converting GTF file to UCSC-styled bed file
... Hello, I have a gff file and I wnt to convert it to UCSC styled bed file ( tab separated, 12-column). Does any one know a reliable tool that can be used for this conversion? Thanks in advance ...
genome next-gen rna-seq written 7 weeks ago by Javad0 • updated 7 weeks ago by genecats.ucsc420
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Tools for Saturation analysis and gene body coverage analysis
... Hello, I have a set of RNA-seq data and I want to perform saturation analysis and gene body coverage analysis on them. Which tools can I use for this type of analysis? Thanks ...
rna-seq written 9 weeks ago by Javad0 • updated 6 weeks ago by Biostar ♦♦ 20

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