group arg parse arguments/ added plotheatmap #25
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LeilyR
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Oct 22, 2019
* debugging and improving the computeOrderedMatrix (#23) * started bug fixing in parsetable * debugging and improving the computeOrderedMatrix changes are included changes in formating, adding the groupUsingSample argument as an optional argument with default = all, adding -a and -b arguments for the region to plot before and after the region of interest and adding the possibilty to plot the intermediate matrix (this might need further improvment) * removed unnecessary comments * added group for arg parse (#24) * group arg parse arguments/ added plotheatmap (#25) * added group for arg parse * fixed the situation when plotheatmap is called but the intermedate matrix is not commit message for your changes. Lines starting * updated requirement and readme (#26) * added group for arg parse * fixed the situation when plotheatmap is called but the intermedate matrix is not commit message for your changes. Lines starting * updated the readme and the requirements.yaml files * small update on readme * small fixes in formatting of readme (#27) * added group for arg parse * fixed the situation when plotheatmap is called but the intermedate matrix is not commit message for your changes. Lines starting * updated the readme and the requirements.yaml files * small update on readme * updating readme format * Documentation (#29) * Started writing the README. Installation section * Commented unrevised chunks * changed readme * fixed preClusterMode * removed some prints * changed the config file. Now two entries are needed for the matrix parameters * fixed the clusterign issue * added the number of processors as an optional arugment * removed bedtools test file * Updated some function definitions (tested) * Minor fix * Updated documentation * Updated program name in doc * merged develop and solved conflicts * fixed readme conflict * updated the usage in readme * added help to readme * updated the help message * updated readme * updated readme * update readme * more update on documentation * added required/optional tags to the AddFeatureToMatrix arguments * renamed AddFeature to addFeature, added documentation for the defs in parseTables, updated readme, changed the version number, added extra argumnets to save the closest genes bed file, set the default referencePoint for finding the closest gene to None * added renamed files
LeilyR
added a commit
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Apr 23, 2020
* debugging and improving the computeOrderedMatrix (#23) * started bug fixing in parsetable * debugging and improving the computeOrderedMatrix changes are included changes in formating, adding the groupUsingSample argument as an optional argument with default = all, adding -a and -b arguments for the region to plot before and after the region of interest and adding the possibilty to plot the intermediate matrix (this might need further improvment) * removed unnecessary comments * added group for arg parse (#24) * group arg parse arguments/ added plotheatmap (#25) * added group for arg parse * fixed the situation when plotheatmap is called but the intermedate matrix is not commit message for your changes. Lines starting * updated requirement and readme (#26) * added group for arg parse * fixed the situation when plotheatmap is called but the intermedate matrix is not commit message for your changes. Lines starting * updated the readme and the requirements.yaml files * small update on readme * small fixes in formatting of readme (#27) * added group for arg parse * fixed the situation when plotheatmap is called but the intermedate matrix is not commit message for your changes. Lines starting * updated the readme and the requirements.yaml files * small update on readme * updating readme format * Documentation (#29) * Started writing the README. Installation section * Commented unrevised chunks * changed readme * fixed preClusterMode * removed some prints * changed the config file. Now two entries are needed for the matrix parameters * fixed the clusterign issue * added the number of processors as an optional arugment * removed bedtools test file * Updated some function definitions (tested) * Minor fix * Updated documentation * Updated program name in doc * merged develop and solved conflicts * fixed readme conflict * updated the usage in readme * added help to readme * updated the help message * updated readme * updated readme * update readme * more update on documentation * added required/optional tags to the AddFeatureToMatrix arguments * renamed AddFeature to addFeature, added documentation for the defs in parseTables, updated readme, changed the version number, added extra argumnets to save the closest genes bed file, set the default referencePoint for finding the closest gene to None * added renamed files * resolved the conflict with master * Readme (#31) * updated readme, added an image * changed the image's extension * added the png image * removed the pdf image * changed the place of the image in readme * added caption for the image * center image * removed the other image. resized the center image * fixed the image caption * more on caption * firxed partitions * typo * Readme (#32) * updated readme, added an image * changed the image's extension * added the png image * removed the pdf image * changed the place of the image in readme * added caption for the image * center image * removed the other image. resized the center image * fixed the image caption * more on caption * firxed partitions * typo * corrected readme text Co-authored-by: Leily Rabbani <rabbani@pc390.ie-freiburg.mpg.de>
LeilyR
added a commit
that referenced
this pull request
Aug 21, 2020
* debugging and improving the computeOrderedMatrix (#23) * started bug fixing in parsetable * debugging and improving the computeOrderedMatrix changes are included changes in formating, adding the groupUsingSample argument as an optional argument with default = all, adding -a and -b arguments for the region to plot before and after the region of interest and adding the possibilty to plot the intermediate matrix (this might need further improvment) * removed unnecessary comments * added group for arg parse (#24) * group arg parse arguments/ added plotheatmap (#25) * added group for arg parse * fixed the situation when plotheatmap is called but the intermedate matrix is not commit message for your changes. Lines starting * updated requirement and readme (#26) * added group for arg parse * fixed the situation when plotheatmap is called but the intermedate matrix is not commit message for your changes. Lines starting * updated the readme and the requirements.yaml files * small update on readme * small fixes in formatting of readme (#27) * added group for arg parse * fixed the situation when plotheatmap is called but the intermedate matrix is not commit message for your changes. Lines starting * updated the readme and the requirements.yaml files * small update on readme * updating readme format * Documentation (#29) * Started writing the README. Installation section * Commented unrevised chunks * changed readme * fixed preClusterMode * removed some prints * changed the config file. Now two entries are needed for the matrix parameters * fixed the clusterign issue * added the number of processors as an optional arugment * removed bedtools test file * Updated some function definitions (tested) * Minor fix * Updated documentation * Updated program name in doc * merged develop and solved conflicts * fixed readme conflict * updated the usage in readme * added help to readme * updated the help message * updated readme * updated readme * update readme * more update on documentation * added required/optional tags to the AddFeatureToMatrix arguments * renamed AddFeature to addFeature, added documentation for the defs in parseTables, updated readme, changed the version number, added extra argumnets to save the closest genes bed file, set the default referencePoint for finding the closest gene to None * added renamed files * resolved the conflict with master * Readme (#31) * updated readme, added an image * changed the image's extension * added the png image * removed the pdf image * changed the place of the image in readme * added caption for the image * center image * removed the other image. resized the center image * fixed the image caption * more on caption * firxed partitions * typo * Readme (#32) * updated readme, added an image * changed the image's extension * added the png image * removed the pdf image * changed the place of the image in readme * added caption for the image * center image * removed the other image. resized the center image * fixed the image caption * more on caption * firxed partitions * typo * corrected readme text Co-authored-by: Leily Rabbani <rabbani@pc390.ie-freiburg.mpg.de>
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