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• Finding All The Genes That Are In A Given Set Of Genomic Co-Ordinates Using R
  Hi, So I've got a list of chromosome segments amplified and deleted by sample with the chromoso...
• identify amplified genes from GISTIC2.0
  As I used GISTIC2.0 to deal with SNP6.0 profiles. I got result files, in which showed the amplifi...
• JISTIC excluded regions
  Hi everyone! I am a graduate student, and my lab models breast cancer in mice. The mice have an ...
• Pathway analysis with co-variates for RNA-seq data
  Hi all, I was wondering if someone knows of a tool to perform a pathway analysis with co-variat...
• Web Resources To Find Cancer Indication Where A Given Gene Is Amplified
  I would like to know if someone is aware of a web application that would give indication or patie...
• Find all sequence of a specific genus amplified by a couple of primers
  Is there a way to find every sequence present in a database amplified by a couple of custom prime...
• Amp/Del genes in GISTIC2.0 output but not covered in original exome-seq baits
  Hi all, I am using GISTIC 2.0 to summarize my targeted exome sequencing data on 30 samples. The ...
• Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
  I have spend sometime trying to understand/analyze exome CNV (copy number variation). There are m...
• Mirna Or Tf Enrichment, Onlinedatabase? Webserver? Local Database?
  Hi all, I get a set of co-expressed genes, since co-expressed genes are mainly due to regulation...
• Extract coordinates of adjacent genes for each provided intergenic regions from gff file
  I have gff files and files containing intergenic regions for different bacterial genomes. I want ...
• Copy number differences between groups
  Analogous to differential expression with RNA data, is there a statistic or tool to analyze the f...
• Recurrent Segmentation Errors
  I'm currently using cnvkit on around 100 paired exome samples. I ran a GISTIC analysis and found ...
• Co-expression analysis for genes coexpressed with gene X, genes X and Y, etc.
  Hi, I have been asked to perform a co-expression analysis to look for genes that are co-expressed...
• GISTIC input parameters.
  Hi everyone I am running GISTIC 2.0 in segmentation data from TCGA and I was wondering whether i...
• Gene Co-expression Tools
  Hello all, Can anyone suggest any gene co-expression tools out there. Also can I use gene co-exp...
• Plotting copy number varation: amplification and deletion data from GISTIC
  Hi there,  I have carried out GISTIC on some Agilent 244K tumour data. I now have the G-scores f...
• GISTIC results. Too many deleted genes?
  Hi all I am kind of sceptical about some results I got from GISTIC 2.0. Using the following par...
• Mutational analysis on 10X scRNA-seq 3' v3 library
  Hello, I have a 10X scRNA-seq 3' v3 library. I would now like to assess whether certain cells in ...