Coffalyser v8
Download the latest Coffalyser MLPA analysis packs here. Since V7 there are two packs, a complete version which requires installing and thus administrator right. Installation of the software is HIGHLY recommended!
This version contains all options including usage of a database system and MLPA mix results merging and automatic calculation of duplos and triplos on results summary files.
The second pack is a zipped file and is the light version of the coffalyser, which doesn't need any installation. Windows vista users are recommended to install the FUll version and then switch of DATABASE usage, by changing use Database usage on the sheet MACRO SETTINGS to $NO.
Both versions include a Coffalyser Manual and test data. Before starting with the program you need to adjust a few Excel settings, instructions can be found in the excel preparation manuals.
The Coffalyser Sheet update is a zip file containing the latest MLPA mix sheets for updating your Coffalyser version. Unzip the file and copy the relevant sheet into the folder called 'MLPA mixes' which can be found at the root of your installed Coffalyser version.
The Coffalyser sample plate generator is a Excel macro which can be used to automatically create plate files for CEQ and ABI systems. This is a time saver on manually adding all the sample names in the capillary run software and also provides several tags for MLPA data organization. Instructions on using this tool can be found in the manuals folder coming with the ZIP file.
To save the following files to disk, right mouse click, Save Target As.
Update to v9.4 to import the size called fragment list file of the FSA reader, updated autobin function, export of statistical files and heatmap images.. You can simply replace the old xls file in the folder where you installed the software.
Note that this version also loads the default settings as applied on the sheet (COLUMN X-Z), you can use the cells to define your personal settings for data filtering and analysis which are then set as default. Using the user defined method during the analysis will allow you to keep analysis settings from the sheet while other methods will overwrite the methodology.
Previous Versions
Previous versions often proved to be more stable with different Office versions or languages. These versions do not require installation and can also be ran from USB devices.
The Coffalyser Sheet update is a zip file containing the latest MLPA mix sheets for updating your Coffalyser version. Unzip the file and copy the relevant sheet into the folder called 'MLPA mixes' which can be found at the root of your installed Coffalyser version.
The Coffalyser sample plate generator is a Excel macro which can be used to automatically create plate files for CEQ and ABI systems. This is a time saver on manually adding all the sample names in the capillary run software and also provides several tags for MLPA data organization. Instructions on using this tool can be found in the manuals folder coming with the ZIP file.
To save the following files to disk, right mouse click, Save Target As.
Coffalyser v9.4 Download Pack
Last Update 200908, includes most relevant manuals and protcols. Also contains all MLPA mix sheets updates to 200908. Install the file to a read/write free location directly on your HD, preferably not in the MyDocument, Program Folder or Desktop location.OLD Coffalyser v8 Download Packets
Version v8 resolves several problems found in v7. V8 furthermore includes direct analysis methods which are only recommended when no difference in signal sloping is found between reference and sample runs. For copy number there is a direct normalization based on contol probes and on all probes. For methylations status analysis a direct methylation status analysis may always be recommended since the same DNA was used and thus sloping can also be expected to be equal. At the settings tab you may futhermore cut imported file names automatically down using numerical or string recognition. More info on the new features in v8 can be found in the Coffalyser v8 Manual(under construction) and in the About the analysis METHODS Note (under construction) .Update to v9.4 to import the size called fragment list file of the FSA reader, updated autobin function, export of statistical files and heatmap images.. You can simply replace the old xls file in the folder where you installed the software.
Note that this version also loads the default settings as applied on the sheet (COLUMN X-Z), you can use the cells to define your personal settings for data filtering and analysis which are then set as default. Using the user defined method during the analysis will allow you to keep analysis settings from the sheet while other methods will overwrite the methodology.
Previous Versions
Previous versions often proved to be more stable with different Office versions or languages. These versions do not require installation and can also be ran from USB devices.
- Coffalyser v3 (zip 3.8MB)
- Coffalyser v3.7 complete (zip 16MB) Stable
- Coffalyser v3.7 light (zip 3.5 MB)
- Coffalyser v5 (zip 8 MB) Stable
Coffalyser Sheet Update
Excel Preparation Manuals
Referring
If you want to refer to the Coffalyser software then please do to the following article (in press). This paper contains more details on the applied methodology behind the Coffalyser software.-
Cellular Oncology 00 (2008) 113 1
DOI 10.3233/CLO-2008-0428
IOS Press
MLPAnalyzer: Data analysis tool for reliable automated normalization of MLPA fragment data.
Jordy Coffa a,c,, Mark A. van de Wiel a,b,d, Begoņa Diosdado a, Beatriz Carvalho a, Jan Schouten c and Gerrit A. Meijer a
a Tumour Profiling Unit & Micro Array Facility, Department of Pathology (Tumor Profiling Unit), VU University Medical Center, Amsterdam, The Netherlands b Department of Biostatistics, Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands c MRC-Holland, Amsterdam, The Netherlands d Department of Mathematics, VU University, Amsterdam, The Netherlands
Coffalyser Sample Plate Generator (S.P.G.)
Download the Coffalyser Sample Plate Generator from here. The SPG requires the same macro security demands as the Coffalyser does, unzip the file to your harddisk and then run the S.P.G. file to start the program.
Please read the instructions in the manuals file before starting for several machine specific run settings should be synchonized from your capillary sequencer device into the sofware to make optimal use of the software.
Coffalyser VB FSA READER (TESTERS ONLY!)
We are working very hard to create a stand alone analysis software which can read and analyse raw data file directly from the capillary sequencer.
A first beta version which can read fsa files and convert them to csv fragment lists can be downloaded here.
To import these csv fragments lists you need to update your xls file with the coffalyser 8.4 xls file. (under construction) .