User: Pappu

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Pappu1.8k
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Posts by Pappu

<prev • 379 results • page 1 of 38 • next >
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iTRAQ vs RNA-seq
... I was trying to compare the log2 fold change in iTRAQ vs RNA-seq fpkm. Genes which have lfc>3 in RNA-seq, have lfc slightly higher than 1. I am wondering if it makes sense. ...
rna-seq written 4 days ago by Pappu1.8k
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Comment: C: Filtering out low expressed genes in RNA-Seq data
... 1 fpkm is a standard filter. ...
written 8 weeks ago by Pappu1.8k
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Answer: A: Database of mouse ligand receptors
... Check the ligand and receptor paper in nature communication from fantom consortium. ...
written 8 weeks ago by Pappu1.8k
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sleuth differential expression without bootstrap
... I was trying to run sleuth for differential expression analysis. But I don't have the kallisto bootstrap values. I am wondering if it can run without bootstrap estimates. ...
rna-seq written 8 weeks ago by Pappu1.8k
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Genomics book for a computer scientist
... I am looking for books on NGS techniques and basic biology for bioinformatics students from computer science background. ...
chip-seq rna-seq written 8 weeks ago by Pappu1.8k • updated 8 weeks ago by KVC_bioinfo200
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Comment: C: FANTOM gene expression data
... Yes averaging gives weird result as many transcript expression is zero. I just took a sum of transcripts expression for each gene. ...
written 8 weeks ago by Pappu1.8k
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FANTOM gene expression data
... I am looking for FANTOM gene expression data. But I could only find transcript expression in this website: http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/extra/CAGE_peaks_expression/ ...
rna-seq written 8 weeks ago by Pappu1.8k • updated 8 weeks ago by Kevin Blighe7.3k
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next step after differential expression analysis
... I got a list of few hundred genes after runnis standard Deseq2 analysis. I am wondering how to list a few genes to focus on based pathway enrichment and other analysis. I am also looking for suitable tools for that. ...
rna-seq written 9 weeks ago by Pappu1.8k • updated 9 weeks ago by Ron660
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awesome cancer genomics
... I am looking for a awesome list of bioinformatics tools for cancer genomics. I am wondering if there is anything like that. ...
chip-seq rna-seq written 10 weeks ago by Pappu1.8k • updated 10 weeks ago by Kevin Blighe7.3k
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Comment: C: interactive pathway analysis with fold change data
... I know about IPA but that's not free. ...
written 10 weeks ago by Pappu1.8k

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