User: Pappu

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Pappu1.8k
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Posts by Pappu

<prev • 372 results • page 1 of 38 • next >
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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 5 days ago by Pappu1.8k • updated 5 days ago by Ron600
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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 days ago by Pappu1.8k • updated 10 days ago by Kevin Blighe1.2k
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Comment: C: interactive pathway analysis with fold change data
... I know about IPA but that's not free. ...
written 10 days ago by Pappu1.8k
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interactive pathway analysis with fold change data
... I am wondering if there is any free tool for that. Reactome does not seem to have any option to enter fold change data. ...
rna-seq written 11 days ago by Pappu1.8k
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6 follow
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Basic methods in ngs analysis
... I am looking for a summary list of most popular methods or algorithms (NOT a list of 1000+ methods) for ngs data analysis like gatk , gsea , bwa , rsem etc. I am wondering if there is any resource for that. ...
chip-seq rna-seq written 12 days ago by Pappu1.8k
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Converting transcript expression to gene expression
... I am trying to convert transcript expression to gene expression. If I take mean, the results are skewed due to some low expressing transcripts. ...
rna-seq written 13 days ago by Pappu1.8k
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NGS protein-protein interaction network
... I am tyring to build a protein-protein interaction network combining KEGG, RNA-seq and other NGS data for cancer and Alzheimer's. I am wondering if there is any existing well established method (i.e. stochastic) for that. ...
rna-seq written 11 months ago by Pappu1.8k
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regulation of gene expression of a set of genes
... I am trying to find out which transcription factors or enhancers might be involved in regulation of expression of a set of genes in lung cancer. Let me know if there is any good resource for that. ...
chip-seq written 11 months ago by Pappu1.8k • updated 10 months ago by tangming20052.1k
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Finding transcriptional regulators of a gene
... I am trying to find out transactional regulators, transcription factor binding sites, epigenetic modifications, enhancers, miRNA binding etc. of a gene say TP53 highly expressed in cancer. I am wondering if there is any good resource for that. ...
chip-seq rna-seq written 11 months ago by Pappu1.8k • updated 10 months ago by ZhouK.R.0
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regulation of protein expression
... I am trying to find find out which transcription factors, ncRNAs, epigenetic modifications, alternative splicing etc might influence the expression of a protein highly expressed in cancer. Is there any easy way to achieve the goal? ...
chip-seq rna-seq written 11 months ago by Pappu1.8k

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