| Latest version: V1.62i from 22.07.2022 |
|
| 22.07.2022 | Multi-class Kolmogorov-Smirnov test. Non-parametric tests | Multi-class Kolmogorov-Smirnov |
| 29.06.2022 | Venn diagrams: 7 / 8 group Venn graphs. Alternative Heatmap / Circlegraph result views. |
| 22.11.2021 | Co-expression / Relevance analysis with one /two matrices. Main menu | Coexpression | Relevance neetworks |
| 19.06.2021 | CoLoM: Reactome pathways integrated. CoLoM-DB builder added: Transorm Reatome-pathway file, NCBI Gene infom Specie => CoLoM-DB |
| 22.04.2021 | Mantel test: test similarity of (positive, distance) matrices. Main menu | Utilities | Statistic tests | MAntel test |
| 16.03.2021 | List-Venn: Venn analysis for nearly unlimited number of groups. |
| 04.02.2021 | Agreement chart: Visualisation of crosstables. Main menu | Utilities | Agreement chart |
| 19.10.2020 | Diversity indices: Analyze Condition wise (count) diversity in (library screening) matrices. Main menu | Utilities | Statistic tests | Count indices |
| 23.01.2020 | Wrapper for UMAP, a dimensional reduction tool like tSNE / PCR Main menu | Analyze | PCA/tSNE/Umap | umap |
| 22.11.2019 | Enrichement p-values for Venn diagrams. |
| 08.11.2018 | tSNE wrapper added. |
| 16.03.2017 | Kolmogorov-Smirnov test added. Non-paramtric tests | 2-class Kolmogorov-Smirnov A tool to explore the method: Utilities | Statistics test | Kolmorov-Smirnov |
| 08.04.2016 | Resampling tests added. Bootstrap/Jackknife your groups and run t-/ANOVA/Man-Whitney-/Kruskal-Wallace tests. |
| 22.04.2016 | Methylaton tools: Generic changepoint detectors / Segmentation added. |
| 25.03.2016 | NMF added. |
| 17.02.2016 | Methylation tools: - Window shift/ averager. - Feature averages (i.g. average, eg. 200-bp Upstream sites,... |
| 15.09.2015 | Additional classification method Random Forest added (wrapping external tool). |
| 05.07.2015 | File table viewer added ( Utilities | Table/file viewer ) |
| 10.06.2015 | Heatmap density plot viewer - transformation to cumulative density added |
| 29.05.2015 | Weighted Cox Regression for non-proportional hazards added. (Survival | Cox regression) |
| 29.05.2015 | Basic editing function for data matrix in Heatmap viewer: Insert/Delete/Copy/Paste rows or columns, Copy/Paste external data annotations. Custom heatmap color schemes may be freely defined. Manual scaling options |
| 15.05.2015 | Heatmap viewer - Customizable high resolution
histogram / density plot viewer for genes /hybs added |
| 07.03.2015 | Methylation utilties adedd: R-wrapper for extraction of quants from IDat files, BMIQ normalisation Beta, M, CN, M=>Beta, Beta=>M computation M/U missing value imputation |
| 22.09.2015 | More helper functions for generation / optimization of
covariates for cox regression. Forest plot for graphical display of Cox regresson results. |
| 21.01.2014 | Several helper functions for generation / optiomization of
covariates for cox regression. |
| 18.10.2013 | Wrapper for R's cox regression implemented
(Survival | Cox regressio) |
| 15.05.2013 | Outlier removal: Grubbs test (at p<0.05) may be used
to exclude outliers in f/T-tests, Anova and replica averaging while importing RT-PCR data. |
| 14.05.2013 | Exclusion of non-numeric values in statistics calculation: SUMO now excludes non numeric values from stattistic calculations (class tests). Thus, non-regular data files (no-microarray data) may be more comfortably analyzed. |
| 14.05.2013 | Import ABI RT-PCR data: Handling of Multiplex controls added. |
| 04.05.2013 | Generic outlier-tester and filter (Grubbs-test) added (Utilities | grubbs outlier removal) |
| 24.04.2013 | Results from "Survival filter 4" analysis is included in an SUMO-analysis file, too. |
| 22.04.2013 | Bug fix: Fixed several prolems in heatmap display Storing of multicolumn annotations colum width, display update after sorting, Custom colors for group bars, ... |
11.04.2013 | Bug fix: workaround for display problems with Windows Themes/Styles |
| 03.04.2013 | Additional classification method added: NBC Naive Bayes Classifier |
28.03.2013 | Additional classification method added: SVM Support Vector machines |
14.03.2013 | Survival filter 4: missing LRT added, more grouping options (perenctile ...), better integration, some bug-fixes |
| 08.03.2013 | Additional classification method added: ANN Artificial Neural netwwork |
| 06.03.2013 | Additional classification method added: Closest centroid |
| 04.03.2013 | Additional classification method added: KNN k-nearest neighbours |
| 27.02.2013 | Classification added: LDA linear discriminant analysis |
12.01.2013 | Several bug-fixes: Network builder; Snapshots in Heatmap, Scatterplot, Histogram window |
| 05.01.2013 | Migration to new compiler: Delphi XE3 |
| 12.06.2012 | Heatmap-viewer: New correlation distances:
Pearson-JackKnife,Spearman, Kendall's-Tau Centroid-linkage |
| 15.05.2012 | Heatmap-viewer: New Minkowski distances:
Manhattan,Chebyshev |
| 20.04.2012 | Adjust data - Data transformation: Exp2 (rt-PCR-cycles to ratio), Ratio to "intensity" added. |
14.02.2012 | Some bug fixes: COLOM can now work with insufficient Reference/Selection lists, where selection may contain keys nof present in reference. COLOM - KEGG pathway viewer can now handle very large pathway map images. rt-PCR data import : Empty Sample/Probe entries are not used for computation of Mean Rn/CT. |
| 15.03.2012 | COLOM - GO-terms: can be evaluated seperately fort the three main classes(Molecular function, Biological process, Cellular component), avoiding memory overflow problems with the internal database. |
| 01.12.2011 | PTM - Grouping and group names are passed to Heatmap ... and subsequent views. Problems with saving analysis fixed. |
| 09.11.2011 | COLOM : A new p-value column is added to the result tables. This column combines
the enrichement-p-value with a mean of the genes p-value, weighing the enrichemnt of a biological theme with the
significance of it's assigned genes. To use this feature supply a gene list: - one line per gene - tab delimited: Gene, Regulation, p-value |
| 12.11.2011 | COLOM now supports also Metabolites (not only genes symbols) with KEGG pathways. |
| 05.11.2011 | During import of exported ABI-SDS ampification data files SUMO non numerical values
(e.g. "not determined") for ct-values are automatically replaced by "40.000". Genes or conditions where there are not
in all cases ct-values found are searched. Such missing values might due to incosistent sample or probe-set names accross
multiple measured plates. |
| 25.10.2011 | Bug fix: Import of CR delimited text files enabled.
Normally, lines in standard text files are delimited by CR-LF (Carriage return + Line Feed)
characters (in e.g. Microsoft based operation systems ) or with Line Feed only (UNIX based OS). Some strange systems may also create CR only delimited files. These may be used with SUMOnow too. |
| 05.10.2011 | During import of exported ABI-SDS ampification data files SUMO computes
means and standard deviation for RN and CT values from all samples of a particular gene. Those values are added
as gene annotations to the data matrix. |
| 05.09.2011 | Import of multiple exported ABI-SDS ampification data files enabled. !!! NB: Values from replicated gene/sample names in the multiple source files will automatically be averaged !!! In case you want to use genes for inter-plate quality tracking you should name such genes like "ACT-Plate1" ... |
| 31.08.2011 | Loading of Comma-Separated-Value (CSV) data tables added Main menu | Open data | Set file type to "Comma separated text (*.csv)" |
| 24.08.2011 | Colom: Download and set up of data bases for GO, KEGG, Chromomal localisation Colom | Preferences Tab | Donwmloa and install ... Button |
| 22.08.2011 | Search genes in SUMO main program Main menu | Analyse | Find genes |
| 17.08.2011 | Demo data sets added Synthetic dataset, Real gene expression, Random data Main menu | Utilities | Demo data | ... |
| 13.08.2011 | Result browser for splicing analyses added Main menu | Utilities | Splicing viewer |
| 05.08.2011 | Splicing analyser for Exon microarray data added Main menu | Utilities | Splicing index |
| 05.08.2011 | COLOM - KEGG: Automatic download and installation of KEGG pathways in COLOM added. COLOM | Preferences tab | Download and install KEGG database |
| 25.07.2011 | Problem with KEGG pathway images fixed: COLOM now
can load either GIF or PNG formatted pathway images. |
| 22.05.2011 | Replica averaging may be performed with different replica means:. arithmetic-/ geometric-/ median / percentile mean (Main menu | Adjust data | Replica averaging | ...) |
| 17.04.2011 | Data (in form of a tab-delimited expression matrix) may be pasted from clipboard (Main menu | File | Paste Matrix from clipboard> |
| 10.03.2011> | Venn diagrams added.
For details go here |
| 15.02.2011 | Paired samples t-tests added. |
| 02.02.2011 | Direct call of Network Builder from heatmap viewer implemented |
| 15.01.2011 | KEGG pathway map viewer added to COLOM. |
| 15.06.2010 | Gene network builder
implemented. For details go here. |
| 15.05.2010 | New normalisation in
conditons: hybridisation centering, Control
normalisation and centering (Main menu | Adjust Data
Coditions | ... ) |
| 15.04.2010 | Mosaic Scatter plots
implemented ( View | Scatterplots | ... ) |
| 15.03.2010 | Search for control genes
according to Van de Sompele's method (
Main menu | Utilities | Control genes | Van de Sompele |
| 15.02.2010 | Import of ABIs RQ-Manager
Amplification-Data Export files ( Main menu |
Import | ABI rtPCR amplification data ) |
| 15.01.2010 | Dot chart/plot
data viewer added to Heatmap viewer ( Heat map Main menu
| Vew | Dot chart ) |
| 15.01.2009 | Import of EXCEL data sheets added |
| 05.12.2008 | Principal Component Analysis (PCA) added |
| 21.11.2008 | K-Means clustering added. |
| 08.11.2008 | Survivalfilter: Fixed some internal
problems, visualisation "Population map" added,
filtering now via Median survival, accelerated. For details go here |
| 25.10.2008 | COLOM: fixed problem with chromosomal co-localization using Mus
Musculus ideograms (slightly different format compared to Homo Sapiens). |
| 15.10.2008 | Gene lists
- auto generated from analyses, or manually created
from scatter plots - and Boolean operations
between gene lists implemented (AND, NAND, OR, NOR, XOR) |
| 20.09.2008 | COLOM: Term
enrichment tests implemented. For single Biological
themes, or scan over all themes. |
| 10.09.2008 | COLOM: Select
to view only sub-branches or direct children in data
table (context menu Tree | => table) |
| 12.06.2008 | COLOM's data filtering reorganised. Tree and table are filtered independent. All columns may be filtered (like MS-Excel's Auto-filter). Context menu column header | Filter | ... |
| 03.06.2008 | Search for genes supports aliases. Term search returns matches and their tree-paths |
| 28.05.2008 | CoLOcalization Mapper supports additional Gene Alias columns in gene index |
| 16.05.2008 | Data Back-up/Restore added (Main menu | Adjust data | Backup) |
| 10.05.2008 | Principal support for KEGG pathways in Co-localisation mapper added. |
| 28.05.2008 | 2-class prediction (with t-test / U-Mann-Whitney test) implemented |
| 20.04.2008 | Merging of new hybridisations with already loaded data matrix based
on unique gene-id implemented. |
| 10.04.2008 | Several new data adjustment function (z-transformation, mean/median
intensity filter, group pool-normalisation, geometric means for all mean based operations,
Replicate gene averaging, Change sign ...) |
| 29.03.2008 | Graphical Chromosomal-band co-localization viewer implemented |
| 24.03.2008 | Selection in Scatter plots may be converted into SUMO gene lists
and can be logically combined. |
| 19.03.2008 | Scatter plots improved: additional regulation indicators, rhombic
selection, view selection in all open viewers, ... |
| 07.03.2008 | Co-localisation mapper with Chromosomal bands implemented |
| 25.02.2008 | Co-localisation mapper with GO-terms implemented |
| 18.02.2008 | Save Analysis now saves Mann-Whitney and Kruskal-Wallis tests too. |
| 12.02.2008 | Program version check and auto-update (only registered
version) implemented. |
| 02.02.2008 | Prediction cross-validation with 2-class tests (t-test /
U-Mann-Whitney) implemented. |
| 20.12.2007 | Adjust data:
new function Shift all positive: shift whole data
matrix so, that no negative values are remaining. |
| 19.12.2007 | Column patterns for data and gene annotations can be defined for loading
of interlaced or irregular expression data files. |
| 18.12.2007 | Add additional condition; annotations via common
"key" (Main menu | Adjust data | Annotation |
Add condition annotation ) |
| 14.12.2007 | Filtering of genes where mean / median from selected conditions is below
user defined threshold ( Main menu | Adjust data | Filter| Genes | Mena / Median intensities) |
| 11.12.2007 | 2-factor ANOVA
implemented. For details go here<. |
| 20.11.2007 | Kruskal-Wallis
(non-parametric multi-class) test implemented. For details go here. |
| 08.11.2007 | Results of statistical tests are passed as additional
"gene-annotations" to heat map viewer. There, they may be used for filtering. |
| 19.10.2007 | U-/Mann-Whitney test implemented (non parametric 2-class test). For
details go here. |
| 23.09.2007 | Imputation of missing values (e.g. "nan"). For details go
here. |
| 22.09.2007 | Filtering for genes containing too many NAN values added (Main menu | Adjust
data | Filter | Genes | NAN values). For details go here. |
| 21.09.2007 | SUMO recognizes and handles non-numerical data cells (e.g.
"nan" or "13.May"). For data processing they are automatically converted => 0.00 |
| 20.09.2007 | Bug fix: Wrong number of rows
(=genes) when interrupting loading of data matrix. |
| 19.07.2007 | Mai menu | Adjust data
| Genes | Hybridisation | pool normalisation
implemented. For details go here. |
| 28.06.2007 | Correlation maps implemented (Main menu | View | Correlation maps ) |
| 14.06.2007 | Histogram viewer implemented (Main menu | View |Histogram ) |
| 10.05.2007 | Scatter plot viewer implemented ( Main menu | View |
Scatterplots). For details go here. |
| 02.05.2007 | Quantile normalisation implemented (Main menu | Adjust data |
Condition | Quantile normalisation). For details go here. |
| 26.04.2007 | Drag and drop data
files for expression matrices and SUMO analysis files implemented. Last header rows/columns when loading expression matrices are automatically recalled. |
| 15.04.2007 | Parallel processing implemented. Select Main menu | Preferences | Multithreaded to select number of multiprocessing / -threading. Number of processes / threads should not exceed number of CPUs / Cores. Presently only normal T-tests, ANOVA, PTM are supported. |
| 10.04.2007 | Bug fix: Centroid profiles now show real centroids |
| 06.04.2007 | Scripting: Scripting may be used to automate multiple analysis. Supported are t-tests, ANOVA, PTM, multi-class SAM For details go here |
| 05.04.2007 | Kaplan Meier survival curves implemented. For details go here. |
| 04.04.2007 | Statistics auto-run generator implemented. - all single class t-test/SAM may (both unique single groups / all unique combinations of groups) - 2-class t-tests/SAM with pair-wise single groups other will come later. For details go here. |
| 01.03.2007 | Documentation functions implemented. Save working parameters and snapshots of graphs into Word / PDF documents. For details go here. |
| 15.02.2007 | Save and later on load complete analyses. Works for t-test, ANOVA and PTM. SAMs will come later. |
| 09.11.2006 | Box plot of data distribution Select Main menu | View | Box plot to view box plots from all conditions, illustrating signal distribution within the conditions (hybridizations). |
| 08.11.2006 | Data adjustment functions added This functions allow to normalise centre and transform all data in the loaded expression matrix for details go here |
| 28.08.2006 | Group selection dialog: View of detailed condition annotation for selected conditions (Context menu Condition list | View all details) Manage selections (Context menu Button Find | Copy / Paste / Save / Load selection) |
| 25.08.2006 | Group selection Dialog: Find condition: Find NEW, AND, AND NOT, OR, OR NOT added Find special modifiers:
Bug fix: Disappearing numbers in Group List Bug fix: Find history Detailed view of a single condition's annotations Progress bar for all data views, Display may be cancelled with Cancel button. More info in Parameter node of Analysis tree Bug Fix: Memory leak with data tables / huge data sets |
| 16.08.2006 | Display of selected / all conditions in data views |
| 10.08.2006 | Multi-class T-test implemented |
| 15.05.2006 | PTM / Regression response implemented |
| 01.05.2006 | Profile editor for
regression SAM / PTM implemented Web based documentation interfaced |
| 27.04.2006 | Regression SAM implemented |
| 22.04.2006 | Multi-class SAM implemented |
| 17.04.2006 | Two class SAM implemented |
| 12.04.2006 | Single class SAM implemented. |
| 05.04.2006 | Basic WEB-based documentation |
| 01.04.2006 | First versionreleased. |