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Author Commit Message Labels Comments Date
Casey Greene avatarCasey Greene
Ignore html and latex documentation
Patrick Bradley avatarPatrick Bradley
Fixed a problem with OntoShell that prevented it from compiling with gcc
ms70 avatarms70
Much improved tests, logic, and reporting in configure.ac. Enabled
mchikina avatarmchikina
Added src files and a tool, SVMperfer, for using the svmperf library for single gene learning
Chris Park avatarChris Park
modified division by zero handling for precision calculation
Aaron Wong avatarAaron Wong
Updated Combiner documentation
Casey Greene avatarCasey Greene
For qdab files, no .quant should be necessary as it is already contained within the qdab.
pkoppstein avatarpkoppstein
tidyup .hgignore
Casey Greene avatarCasey Greene
add aclocal and configure to hgignore, remove configure (automake generated and requires Makefile.in to run successfully anyway).
Casey Greene avatarCasey Greene
Commit to make the repository internally consistent (automake generated files are excluded as are all Makefile.am files from the tools directory -- cmdline.c and cmdline.h are included).
pkoppstein avatarpkoppstein
Added tag v2.0 for changeset 2b8b9acf64b9
pkoppstein avatarpkoppstein
hg convert --filemap sleipnir-essentials-plus.filemap sleipnir-archive ...
peak avatarpeak
Added tag split for changeset cf46c69cca79
Tags
essentials-plus
Chris Park avatarChris Park
removed automake *.am files
Tags
split
Chris Park avatarChris Park
add to ignore *.o files
Chris Park avatarChris Park
modified a bug that used 'dmissing' flag checking with "_arg" instead of "_given"
mchikina avatarmchikina
Actually added PCL2Bin files
mchikina avatarmchikina
-Added memory mapping support for pcl files
Chris Park avatarChris Park
merge annotation OBO updates, plus PR/RECALL columns to DChecker
Chris Park avatarChris Park
merge Hypergeometric clarifications
Chris Park avatarChris Park
merge support of 'bin' binary PCL files
Chris Park avatarChris Park
merged qdab support and additional functionalities for Dat2Dab
Chris Park avatarChris Park
added .hgignore to ignore deps cache Po etc generated files
Default avatar cgreene
KEGG no longer wraps lines so a substantially larger buffer size is now needed for lines from the ko file.
Default avatar cgreene
Make memory mapping of output files optional via -M flag. This flag affects the inference mode and should only be used if you have sufficient local storage for intermediate networks. Without this flag, it is best to have sufficient RAM for intermediate networks.
Chris Park avatarChris Park
Added new tool MIed, similar to MIer however calculates MI between two dataset only using the union of the two gene sets. In contrast, MIer uses the sum of all genes among all datasets given to calculate MI. MIed allows MI to be constant even after adding new dataset into the integration.
Curtis Huttenhower avatarCurtis Huttenhower
Fix bug in CDat::Open( CDat, vector<CGenes>*, ... ) for importing known negatives
Default avatar chut...@hutlab3.sph.harvard.edu
Improve COALESCE termination criteria (slightly more permissive)
Default avatar psa...@hutlab3.sph.harvard.edu
Divided the code execution in two different stages: training and prediction
Default avatar psa...@hutlab3.sph.harvard.edu
Seperated the execution in two stages: Training and Learning
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