https://sourceforge.net/p/ipig/wiki/iPiG%2520GUI/Recent changes to iPiG GUIenThu, 29 Mar 2012 11:20:24 -0000https://sourceforge.net/p/ipig/wiki/iPiG%2520GUI/<pre>--- v7 +++ v8 @@ -1,5 +1,5 @@ This gives an overview how to run a mapping with the iPiG GUI. -For more details about the data formats look at the corresponding wiki page: [Data Formats] +For more details about the data formats look at the corresponding wiki page: [Input Formats]  </pre>Mathias KuhringThu, 29 Mar 2012 11:20:24 -0000https://sourceforge.net9852d919db7ac3530c54187bb7a89e6620980f3dhttps://sourceforge.net/p/ipig/wiki/iPiG%2520GUI/<pre>--- v6 +++ v7 @@ -19,7 +19,7 @@ * **UniProt ID-mapping file (optional but recommended)** * Indicate the Uniprot ID-mapping file (tab-delimited table) * **Proteome fasta file (optional)** - * Indicate a Uniprot proteosom in fasta format + * Indicate a Uniprot proteome in fasta format Export Settings --------------- </pre>Mathias KuhringTue, 20 Mar 2012 10:33:01 -0000https://sourceforge.nete4e7413af16da0d893b1ec87649d5c60dff7a466https://sourceforge.net/p/ipig/wiki/iPiG%2520GUI/<pre>--- v5 +++ v6 @@ -26,7 +26,7 @@ * **Score range** & **Threshold** * For the outputs give the score range of the PSMs and define thresholds to separate PSMs in three scoring groups * **Colors** - * For the BED output give three RGB colors that indicates the scoring group of each PSM + * For the BED output give three RGB colors that indicates the scoring group of each PSM. Suitable colors (grey, orange, green) are provided by the default configuration file (ipig.conf). Execution --------- </pre>Mathias KuhringMon, 19 Mar 2012 13:41:46 -0000https://sourceforge.net192319eac6138eddb289d507ec82e4a0883c1b75https://sourceforge.net/p/ipig/wiki/iPiG%2520GUI/<pre>--- v4 +++ v5 @@ -1,41 +1,41 @@ -This gives you an overview how to run a mapping with the iPiG GUI. +This gives an overview how to run a mapping with the iPiG GUI. For more details about the data formats look at the corresponding wiki page: [Data Formats]  Input ----- * **Peptide Spectrum Matches** - * Indicate the file with peptide spectrum matches (PSMs) of interest in mzIdentML format + * Indicate the file with peptide spectrum matches (PSMs) of interest in mzIdentML or text format * **Output Path (Optional)** * Specify an output path for the result files (execution path is used by default) Resources --------- * **UCSC/Ensembl Genes table file** - * Indicate a file with reference gene annotations in USCS table format (UCSC or Ensembl genes are supported yet) + * Indicate a file with reference gene annotations in USCS table format (UCSC or Ensembl genes are currently supported) * **UCSC/Ensembl Amino Acid Sequences table file** * Indicate a file with reference amino acid sequences corresponding to the gene annotations file in USCS table format * **UniProt ID-mapping file (optional but recommended)** * Indicate the Uniprot ID-mapping file (tab-delimited table) * **Proteome fasta file (optional)** * Indicate a Uniprot proteosom in fasta format Export Settings --------------- * **Score range** & **Threshold** * For the outputs give the score range of the PSMs and define thresholds to separate PSMs in three scoring groups * **Colors** * For the BED output give three RGB colors that indicates the scoring group of each PSM Execution --------- * **Start** * Run the mapping by pressing the Start-button Configuration ------------- * **Load** * Load a configuration file to import the parameters for Resources and Export Settings * **Save** - * Save a configuration file to keep your choosen Resources and Export Settings + * Save a configuration file to keep the selected Resources and Export Settings </pre>Mathias KuhringMon, 19 Mar 2012 13:32:05 -0000https://sourceforge.net50dc1bc8e82d107b4c4a9cc073eaf2ec7c93132chttps://sourceforge.net/p/ipig/wiki/iPiG%2520GUI/<pre></pre>Mathias KuhringSat, 17 Mar 2012 07:56:32 -0000https://sourceforge.netdaf114fd2306cf8889320581da202f02c76c3e8chttps://sourceforge.net/p/ipig/wiki/How%2520to%2520use%2520the%2520iPiG%2520GUI/<pre>--- v2 +++ v3 @@ -1,24 +1,41 @@ This gives you an overview how to run a mapping with the iPiG GUI. - -For more details about the data formats look at the corresponding wiki page:[Data Formats] - +For more details about the data formats look at the corresponding wiki page: [Data Formats] +  -1. Peptide Spectrum Matches +Input +----- +* **Peptide Spectrum Matches** * Indicate the file with peptide spectrum matches (PSMs) of interest in mzIdentML format -* Output Path (Optional) +* **Output Path (Optional)** * Specify an output path for the result files (execution path is used by default) -* UCSC/Ensembl Genes table file + +Resources +--------- +* **UCSC/Ensembl Genes table file** * Indicate a file with reference gene annotations in USCS table format (UCSC or Ensembl genes are supported yet) -* UCSC/Ensembl Amino Acid Sequences table file +* **UCSC/Ensembl Amino Acid Sequences table file** * Indicate a file with reference amino acid sequences corresponding to the gene annotations file in USCS table format -* UniProt ID-mapping file (optional but recommended) +* **UniProt ID-mapping file (optional but recommended)** * Indicate the Uniprot ID-mapping file (tab-delimited table) -* Proteome fasta file (optional) +* **Proteome fasta file (optional)** * Indicate a Uniprot proteosom in fasta format -* Score range & Threshold - *For the outputs give the score range of the PSMs and define thresholds to separate PSMs in three scoring groups -* Colors + +Export Settings +--------------- +* **Score range** & **Threshold** + * For the outputs give the score range of the PSMs and define thresholds to separate PSMs in three scoring groups +* **Colors** * For the BED output give three RGB colors that indicates the scoring group of each PSM -* Start - * Execute the mapping by pushing the Start-button + +Execution +--------- +* **Start** + * Run the mapping by pressing the Start-button + +Configuration +------------- +* **Load** + * Load a configuration file to import the parameters for Resources and Export Settings +* **Save** + * Save a configuration file to keep your choosen Resources and Export Settings </pre>Mathias KuhringFri, 16 Mar 2012 18:12:31 -0000https://sourceforge.net68ade6666cba9a2579f73d95d5983fb43e40f8afhttps://sourceforge.net/p/ipig/wiki/How%2520to%2520use%2520the%2520iPiG%2520GUI/<pre>--- v1 +++ v2 @@ -1,1 +1,24 @@ +This gives you an overview how to run a mapping with the iPiG GUI. + +For more details about the data formats look at the corresponding wiki page:[Data Formats] +  + +1. Peptide Spectrum Matches + * Indicate the file with peptide spectrum matches (PSMs) of interest in mzIdentML format +* Output Path (Optional) + * Specify an output path for the result files (execution path is used by default) +* UCSC/Ensembl Genes table file + * Indicate a file with reference gene annotations in USCS table format (UCSC or Ensembl genes are supported yet) +* UCSC/Ensembl Amino Acid Sequences table file + * Indicate a file with reference amino acid sequences corresponding to the gene annotations file in USCS table format +* UniProt ID-mapping file (optional but recommended) + * Indicate the Uniprot ID-mapping file (tab-delimited table) +* Proteome fasta file (optional) + * Indicate a Uniprot proteosom in fasta format +* Score range & Threshold + *For the outputs give the score range of the PSMs and define thresholds to separate PSMs in three scoring groups +* Colors + * For the BED output give three RGB colors that indicates the scoring group of each PSM +* Start + * Execute the mapping by pushing the Start-button </pre>Mathias KuhringFri, 16 Mar 2012 18:02:21 -0000https://sourceforge.nete5d6eec67a92875b240cb98d644245e3f60abf31https://sourceforge.net/p/ipig/wiki/How%2520to%2520use%2520the%2520iPiG%2520GUI/Mathias KuhringFri, 16 Mar 2012 17:49:45 -0000https://sourceforge.net546eaec3127d3a050c9fa3cc19d8fa69b357106f