| 67 | | || [wiki:se.lu.onk.BaseFile BaseFile] || Other || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz?format=raw 1.0] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.8 || Java utility package for reading the BASEFile format. Required for many se.lu.onk-series plug-ins. [[br]] Not tested with BASE 1.2.17+ but expected to work. || |
| 68 | | || [wiki:se.lu.onk.CGHDataDumper CGH Data Dumper] || Export || || 1.2.17+, 2.8 || Dumps bioassay sets in several formats, useful for non-CGH data as well. [[br]] Not tested with BASE 1.2.17+ but expected to work || |
| 69 | | || [wiki:se.lu.onk.Center Median/mean centering] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.Center/Center-2.1.tgz?format=raw 2.1] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.Center/Center-2.1.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.8 || The center plug-in allows the user to center the expression levels either per gene or per array. [[br]] Not tested with BASE 1.2.17+ but expected to work. || |
| 70 | | || [wiki:se.lu.onk.MergeBioAssay Merge BioAssay] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.MergeBioAssay/MergeBioAssay-2.1.tgz?format=raw 2.1] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.MergeBioAssay/MergeBioAssay-2.1.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.8 || Merge bioassays by grouping them according to annotation types or syntactical differences in the name. [[br]] Not tested with BASE 1.2.17+ but expected to work. || |
| | 67 | || [wiki:se.lu.onk.BaseFile BaseFile] || Other || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz?format=raw 1.0] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz.MD5?format=raw MD5]) || 1.2.17+ [[br]] 2.8 or later || Java utility package for reading the BASEFile format. Required for many se.lu.onk-series plug-ins. [[br]] Not tested with BASE 1.2.17+ but expected to work. || |
| | 68 | || [wiki:se.lu.onk.CGHDataDumper CGH Data Dumper] || Export || || 1.2.17+ [[br]] 2.8 or later || Dumps bioassay sets in several formats, useful for non-CGH data as well. [[br]] Not tested with BASE 1.2.17+ but expected to work || |
| | 69 | || [wiki:se.lu.onk.Center Median/mean centering] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.Center/Center-2.1.tgz?format=raw 2.1] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.Center/Center-2.1.tgz.MD5?format=raw MD5]) || 1.2.17+ [[br]] 2.8 or later || The center plug-in allows the user to center the expression levels either per gene or per array. [[br]] Not tested with BASE 1.2.17+ but expected to work. || |
| | 70 | || [wiki:se.lu.onk.MergeBioAssay Merge BioAssay] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.MergeBioAssay/MergeBioAssay-2.1.tgz?format=raw 2.1] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.MergeBioAssay/MergeBioAssay-2.1.tgz.MD5?format=raw MD5]) || 1.2.17+ [[br]] 2.8 or later || Merge bioassays by grouping them according to annotation types or syntactical differences in the name. [[br]] Not tested with BASE 1.2.17+ but expected to work. || |
| 72 | | || [wiki:se.lu.onk.ReplicateError ReplicateError] || Filter || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.ReplicateError/ReplicateError-1.3.tgz?format=raw 1.3] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.ReplicateError/ReplicateError-1.3.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.8 || Implementation of 'Analysis of replicates' Yang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062 [[br]] http://genomebiology.com/2002/3/11/research/0062 Not tested with BASE 1.2.17+ but expected to work. || |
| 73 | | || [wiki:se.lu.onk.Smooth Smooth] || Transformation || || 1.2.17+, 2.7 || Smooth can be used to reduce experimental noise over a chromosome profile || |
| 74 | | || [wiki:se.lu.onk.VirtualArray Virtual Array] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.VirtualArray/VirtualArray-1.1.tgz?format=raw 1.1] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.VirtualArray/VirtualArray-1.1.tgz.MD5?format=raw MD5]) || 1.2.17+, 2.10 || Create a virtual array design for bioassays. [[br]] Not tested with BASE 1.2.17+ but expected to work. || |
| 75 | | || [wiki:se.lu.thep.WeNNI WeNNI] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/WeNNI/wenni-0.6.tar.gz?format=raw 0.6] || 1.2.17+, 2.6 || A missing value imputation algorithm, Johansson et al. BMC Bioinformatics 2006, 7:306 [[br]] http://www.biomedcentral.com/1471-2105/7/306 || |
| | 72 | || [wiki:se.lu.onk.ReplicateError ReplicateError] || Filter || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.ReplicateError/ReplicateError-1.3.tgz?format=raw 1.3] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.ReplicateError/ReplicateError-1.3.tgz.MD5?format=raw MD5]) || 1.2.17+ [[br]] 2.8 or later || Implementation of 'Analysis of replicates' Yang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062 [[br]] http://genomebiology.com/2002/3/11/research/0062 Not tested with BASE 1.2.17+ but expected to work. || |
| | 73 | || [wiki:se.lu.onk.Smooth Smooth] || Transformation || || 1.2.17+ [[br]] 2.7 or later || Smooth can be used to reduce experimental noise over a chromosome profile || |
| | 74 | || [wiki:se.lu.onk.VirtualArray Virtual Array] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.VirtualArray/VirtualArray-1.1.tgz?format=raw 1.1] ([http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.VirtualArray/VirtualArray-1.1.tgz.MD5?format=raw MD5]) || 1.2.17+ [[br]] 2.10 or later || Create a virtual array design for bioassays. [[br]] Not tested with BASE 1.2.17+ but expected to work. || |
| | 75 | || [wiki:se.lu.thep.WeNNI WeNNI] || Transformation || [http://baseplugins.thep.lu.se/attachment/wiki/WeNNI/wenni-0.6.tar.gz?format=raw 0.6] || 1.2.17+ [[br]] 2.6 or later || A missing value imputation algorithm, Johansson et al. BMC Bioinformatics 2006, 7:306 [[br]] http://www.biomedcentral.com/1471-2105/7/306 || |
