User: Pappu

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Pappu1.9k
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Posts by Pappu

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Comment: C: Gene function prediction
... Nothing came out from uniprot go annotation. ...
written 5 months ago by Pappu1.9k
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Gene function prediction
... I am wondering if there is any good way to predict the function of a gene given the fact that hardly any literature exists on it. ...
chip-seq rna-seq written 5 months ago by Pappu1.9k
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LINCS DE genes
... I am looking for a list of differentially expressed (up and down) genes from all cmap perturbation experiments at clue.io I could only get a small fraction of those from the Enrichr website. I am wondering where can I get such list or how can I generate it from the raw data? ...
rna-seq written 5 months ago by Pappu1.9k
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5 follow
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basic experimental methods book for bioinformaticians
... I am wondering if the is any basic experimental methods book or review for bioinformaticians so that they can understand the presentations given by experimentalists. Such book should include what kind of experimental methods can be used to validate what kind of in-silico analysis results for example ...
next-gen rna-seq written 5 months ago by Pappu1.9k
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top cited bioinformatics papers during last 5 years
... I am wondering if there is any curated list of top cited bioinformatics papers during last 5 years.. ...
next-gen written 5 months ago by Pappu1.9k
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DE and enrichment analysis pipeline
... I am wondering if there is any pipeline which runs DESeq2, EdgeR etc DE analysis and GSEA, Pathway etc enrichment and other basic analysis in one go and make the results available by some kind of shiny or other web app. ...
rna-seq written 6 months ago by Pappu1.9k • updated 6 months ago by EagleEye6.4k
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The effect of various filters on fast RNA-seq quantification
... I am wondering what is the effect of following filters before using fast quantifiers like salmon/kallisto: 1. Adapter trimming 2. Size selection 3. Quality filtering ...
rna-seq written 6 months ago by Pappu1.9k • updated 4 months ago by Biostar ♦♦ 20
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combining reads from multiple lanes for DE analysis
... I am tying to do differential expression (DE) analysis between different conditions. Now I have same samples sequenced at multiple lanes to improve coverage. I am wondering if it would be better to combine those reads from different lanes for quantification or quantify the reads separately before DE ...
rna-seq written 6 months ago by Pappu1.9k • updated 6 months ago by ATpoint21k
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Answer: A: Any database for downloading cancer cell-lines transcriptome differential expres
... Check out https://portals.broadinstitute.org/ccle ...
written 7 months ago by Pappu1.9k
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Answer: A: RNA-Seq database of cancer patients other than TCGA and ICGC?
... Check out http://www.cbioportal.org/ ...
written 7 months ago by Pappu1.9k

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Popular Question 4 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
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