Co-expression network analysis using RNA-Seq data

DC ISCB Workshop 2016 – Co-expression network analysis using RNA-Seq data (Keith Hughitt)

Tutorial on Co-expression network analysis using RNA-Seq data presented at the ISCB DC Regional Student Group Workshop at the University of Maryland – College Park (June 15 2016).

In this presentation, I provide a simple overview of co-expression network analysis, with an emphasis on the use of RNA-Seq data. A motivation for the use of co-expression network analysis is provided and compared to other common types of RNA-Seq analyses such as differential expression analysis and gene set enrichment analysis. The use of adjacency matrices to represent networks is explored for several different types of networks and a small synthetic dataset is used to demonstrate each of the major steps in co-expression network construction and module detection. The tutorial portion of the presentation then applies some of these principles using a real dataset containing ~3000 genes, after filtering.

Links
———
[1] Meeting site: https://iscb-dc-rsg.github.io/2016-su…
[2] Tutorial: https://github.com/iscb-dc-rsg/2016-s…
[3] Slides: http://khughitt.github.io/2016-iscb-d…

Leave a Reply

Your email address will not be published. Required fields are marked *

*

Time limit is exhausted. Please reload CAPTCHA.


Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(http://api.facebook.com/restserver.php?method=links.getStats&format=json&urls=https%3A%2F%2Fwww.rna-seqblog.com%2Fsingle-cell-rna-sequencing-and-multiple-myeloma-2%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179

Warning: file_get_contents(http://urls.api.twitter.com/1/urls/count.json?url=https%3A%2F%2Fwww.rna-seqblog.com%2Fsingle-cell-rna-sequencing-and-multiple-myeloma-2%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179

Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(http://api.facebook.com/restserver.php?method=links.getStats&format=json&urls=https%3A%2F%2Fwww.rna-seqblog.com%2Fmulti-omics-bioinformatics-platform-processing-analysis-and-integration%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179

Warning: file_get_contents(http://urls.api.twitter.com/1/urls/count.json?url=https%3A%2F%2Fwww.rna-seqblog.com%2Fmulti-omics-bioinformatics-platform-processing-analysis-and-integration%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179

Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(http://api.facebook.com/restserver.php?method=links.getStats&format=json&urls=https%3A%2F%2Fwww.rna-seqblog.com%2Fbroad-distribution-spectrum-from-gaussian-to-power-law-appears-in-stochastic-variations-in-rna-seq-data%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179

Warning: file_get_contents(http://urls.api.twitter.com/1/urls/count.json?url=https%3A%2F%2Fwww.rna-seqblog.com%2Fbroad-distribution-spectrum-from-gaussian-to-power-law-appears-in-stochastic-variations-in-rna-seq-data%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179

Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(http://api.facebook.com/restserver.php?method=links.getStats&format=json&urls=https%3A%2F%2Fwww.rna-seqblog.com%2Fnew-tool-enables-big-scale-analysis-of-single-cell-rna-seq-data%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179

Warning: file_get_contents(http://urls.api.twitter.com/1/urls/count.json?url=https%3A%2F%2Fwww.rna-seqblog.com%2Fnew-tool-enables-big-scale-analysis-of-single-cell-rna-seq-data%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179

Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(http://api.facebook.com/restserver.php?method=links.getStats&format=json&urls=https%3A%2F%2Fwww.rna-seqblog.com%2Fscientist-i-computational-analysis-of-cell-types-in-human-brain-using-single-nucleus-rna-sequencing%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 121

Warning: file_get_contents(): http:// wrapper is disabled in the server configuration by allow_url_fopen=0 in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179

Warning: file_get_contents(http://urls.api.twitter.com/1/urls/count.json?url=https%3A%2F%2Fwww.rna-seqblog.com%2Fscientist-i-computational-analysis-of-cell-types-in-human-brain-using-single-nucleus-rna-sequencing%2F): failed to open stream: no suitable wrapper could be found in /home/rnaseqbl/public_html/wp-content/plugins/most-shared-posts/msp-fetch.php on line 179