DAPPLE Updates
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3/11/2011:
-CI scores are now bonferroni corrected for the number
of CIs. This is a rather harsh correction, since the number of CIs
can be in the 1000s and the best p-value DAPPLE can achieve is 1/10001,
corresponding to 10,000 permutations. Thus we suggest rank-ordering
CIs to prioritize interesting ones, or relaxing your p-value
cutoff. To remove this correction, divide the p-values by the number
of CIs.
-SeedScore files are now sorted by p-value, there was a
bug that prevented this.
-Iterate files now show up in the
results section of the status update page, there was a bug that
prevented this.
-You can now return to the main DAPPLE page from
the status update page.
4/20/2011:
-The plot now has a legend to help match colors to
region IDs.
5/25/2011:
-The common interactor file (*_CI) now outputs the
number of disease proteins that the common interactor binds to. This
is useful if you would like to prioritize common interactors by this
value.
5/27/2011:
-The "nearest gene" option. This may be of interest to
people who are inputing a list of SNPs and would like to use only the
gene closest to each SNP, rather than all genes in the LD
wingspan. This option is not relevant to other types of input,
including genes, regions and genes with a region tag.
6/6/2011:
-Fixed a small bug. If the user
inputs overlapping regions, they weren't being merged properly in some
instances. This is now fixed.
8/23/2011:
-Optimized the code to be a bit
faster, which required re-writing of a substantial portion. Please
report any bugs to dapple@broadinstitute.org.
8/23/2011:
-We have implemented a new
plotting function which will automatically appear on the results
page. The benefit to this new function is that it is interactive. You
can click on nodes to drag and drop them to a desired location. We are
still fixing this up, but we hope that it drastically improves some of
the visualization problems with large networks.
10/12/2011:
-A regulatory region flag has been
put in place. This applies only to SNPs or regions as inputs. When DAPPLE
looks for genes that overlap an input region (either defined from a SNP or
explicitly as a region), it adds a default 50kb upstream and 50kb downstream
to the gene. The reason is that causal variation can affect regulatory
regions, so we'd like to capture that. Now, you can choose how big you'd
like that regulatory region to be!
-We also spruced up the site a bit - changed a few pull downs to
check boxes, added descriptions where needed, and added an option to receive
emails about DAPPLE updates.
-We now allow input of virtually all description types. DAPPLE will
automatically strip any non-alphanumeric characters or spaces, however. For
example, "test_genes 2" would become "testgenes2".
4/6/2013:
-Indirect connections are now available in the results as a text file.