User: Pappu

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Pappu1.9k
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Posts by Pappu

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22
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5
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390
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10 follow
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Useful productivity tools for bioinformaticians
... I am wondering which productivity tools you use as a bioinformatician to improve the productivity of day to day work. For example using git, nextflow etc. ...
R next-gen chip-seq rna-seq python written 6 months ago by Pappu1.9k • updated 6 months ago by Joe17k
0
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1
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190
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1
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Comment: C: DE Analysis of Protein Coding Genes
... Human gencode outputs ~60k genes. ...
written 9 months ago by Pappu1.9k
2
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1
answer
190
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1
answer
DE Analysis of Protein Coding Genes
... I am wondering if it is a standard practice to only include ~20k protein coding genes for DE and subsequent pathway analysis? ...
rna-seq written 9 months ago by Pappu1.9k
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0
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404
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0
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Comment: C: Gene function prediction
... Nothing came out from uniprot go annotation. ...
written 15 months ago by Pappu1.9k
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0
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404
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0
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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 15 months ago by Pappu1.9k
0
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0
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258
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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 15 months ago by Pappu1.9k
2
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0
answers
431
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5 follow
0
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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 16 months ago by Pappu1.9k
3
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0
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786
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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 16 months ago by Pappu1.9k
1
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1
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487
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1
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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 17 months ago by Pappu1.9k • updated 17 months ago by EagleEye6.6k
4
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0
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294
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0
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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 17 months ago by Pappu1.9k • updated 15 months ago by Biostar ♦♦ 20

Latest awards to Pappu

Popular Question 5 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Popular Question 5 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Popular Question 7 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Popular Question 9 months ago, created a question with more than 1,000 views. For cancer genes database
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Popular Question 12 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Great Question 12 months ago, created a question with more than 5,000 views. For Easiest way to convert python script to web application
Popular Question 15 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Popular Question 15 months ago, created a question with more than 1,000 views. For cancer genes database
Popular Question 16 months ago, created a question with more than 1,000 views. For cancer genes database
Popular Question 17 months ago, created a question with more than 1,000 views. For cancer genes database
Popular Question 18 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Popular Question 19 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Popular Question 19 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Popular Question 21 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Popular Question 22 months ago, created a question with more than 1,000 views. For Assembled TCGA dataset download
Popular Question 22 months ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Finding overlap between BAM files or BAM and gff3 files
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Difference between MrBayes and Beast MCC tree
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Finding overlap between BAM files or BAM and gff3 files
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Assembled TCGA dataset download
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Estimating tumor purity from genomic data
Appreciated 2.2 years ago, created a post with more than 5 votes. For ipython notebooks on bioinformatics and genomics

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