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Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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author proteore
date Fri, 01 Jun 2018 11:10:47 -0400
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1 Wrapper for Filter by keywords or numerical values Tool 1 Wrapper for Filter by keywords or numerical values Tool
2 ======================================================= 2 =======================================================
3 3
4 **Authors** 4 **Authors**
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6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 6 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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10 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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14 ------------------------------------------------------- 14 -------------------------------------------------------
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16 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). 16 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output).
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18 **For each row, if there are more than one protein IDs/protein names/gene names, only the first one will be considered in the output** 18 **Filter by keyword(s)**
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20 **Filter the file by keywords**
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22 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. 20 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords.
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24 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175 22 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175
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44 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. 42 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed.
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46 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. 44 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed.
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48 **Filter the file by values** 46 -------------------------------------------------------
49 47
50 You can choose to use one or more options (e.g. to filter out peptides of low intensity value, by q-value, etc.). 48 **Filter by values**
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52 * For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option. 50 You can filter your data by a column of numerical values.
51 Enter the column to be use and select one operator in the list :
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53 - "="
54 - "!="
55 - "<"
56 - "<="
57 - ">"
58 - ">="
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60 Then enter the value to filter and specify the column to apply that option.
61 If a row contains a value that correspond to your settings, it will be filtered.
62
63 -------------------------------------------------------
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65 **Filter by a range of values**
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67 You can also set a range of values to filter your file.
68 In opposition to value filter, rows with values inside of the defined range are kept.
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70 Rows with values outside of the defined range will be filtered.
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72 -------------------------------------------------------
73
74 **AND/OR operator**
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76 Since you can add as many filters as you want, you can choose how filters apply on your data.
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78 AND or OR operator option works on all filters :
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80 - OR : only one filter to be satisfied to remove one row
81 - AND : all filters must be satisfied to remove one row
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83 -------------------------------------------------------
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85 **Sort the results files**
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87 You can sort the result file if you wish, it can help you to check results.
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89 In order to do so : enter the column to be used, all columns will be sorted according to the one filled in.
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91 Rows stay intact, just in different order like excel.
92 You can also choose ascending or descending order, by default descending order is set.
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94 -------------------------------------------------------
53 95
54 **Output** 96 **Output**
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56 The tool will produce 2 output files. 98 The tool will produce 2 output files.
57 99