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				<h4>
					Tutorial: <a target="_blank"
						href="http://www.broadinstitute.org/achilles">Project Achilles</a>
					and the <a target="_blank"
						href="http://www.broadinstitute.org/ccle/home">Cancer Cell
						Line Encyclopedia (CCLE)</a> datasets.
				</h4>
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				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Open
					Project Achilles Gene Essentiality Scores</a>
				<p class="collapse">Open the Project Achilles gene essentiality
					scores under the preloaded datasets section. By default, values in
					the heat map are mapped to colors using the minimum and maximum of
					each row independently.</p>




				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Median
					Absolute Deviation (MAD)</a>
				<p class="collapse">
					Click the tools icon
					<button type="button"
						class="btn btn-default btn-xs dropdown-toggle">
						<span class="fa fa-wrench"></span> <span class="fa fa-caret-down"></span>
					</button>
					and select "Create Calculated Annotation". <br /> Enter "MAD" for
					the "Annotation name". <br /> Enter "MAD()" for "Formula" and
					click "OK". <br /> A new row annotation named "MAD" will appear to
					the right of the heat map.
				</p>

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Filter
					Rows</a>
				<p class="collapse">
					Show only the top 500 most variable genes by the median absolute
					deviation <br /> Click the filter icon
					<button type="button"
						class="btn btn-default btn-xs dropdown-toggle">
						<span class="fa fa-filter"></span> <span class="fa fa-caret-down"></span>
					</button>
					. <br />Click the "Add" button and set the field name to "MAD". <br />Click
					"Switch to top N filter" and enter "500" for "N". Note that 523
					rows are now shown because of ties in the median absolute
					deviation.
				</p>

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Hierarchical
					Clustering</a>
				<p class="collapse">
					Click the tools icon
					<button type="button"
						class="btn btn-default btn-xs dropdown-toggle">
						<span class="fa fa-wrench"></span> <span class="fa fa-caret-down"></span>
					</button>
					and select "Hierarchical Clustering". Change "Cluster" to "Rows and
					columns". Click "OK" to run the analysis. <br /> Do haematopoietic
					cell lines cluster together? Hover over the primary_site
					annotations to highlight cell lines from the same primary site. You
					can dynamically cut the dendrogram by dragging the dashed line at
					the top of the dendrogram. <br />Hierarchical clustering
					recursively merges objects based on their pair-wise distance.
					Objects closest together are merged first, objects furthest apart
					are merged last. The result is a tree structure, referred to as a
					dendogram, where the leaf nodes represent the original items and
					internal (higher) nodes represent the merges that occurred. Click <a
						target="_black"
						href="http://www.mathworks.com/help/stats/hierarchical-clustering.html">here</a>
					for a more detailed description of the hierarchical clustering
					algorithm and <a target="_blank"
						href="http://support.minitab.com/en-us/minitab-express/1/help-and-how-to/modeling-statistics/regression/supporting-topics/basics/a-comparison-of-the-pearson-and-spearman-correlation-methods/">here</a>
					for a comparison of the Pearson and Spearman correlation methods.
				</p>

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Compress
					Heat Map</a>
				<p class="collapse">
					Click the fit to window icon
					<button type="button" class="btn btn-default btn-xs">
						<span class="fa fa-compress"></span>
					</button>
					to fit compress the heat map. Click
					<button type="button" class="btn btn-default btn-xs"
						title="Reset Zoom" name="resetZoom">100%</button>
					to return to the normal heat map size.
				</p>

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Remove
					Row Filter</a>
				<p class="collapse">
					Click the filter icon
					<button type="button"
						class="btn btn-default btn-xs dropdown-toggle">
						<span class="fa fa-filter"></span> <span class="fa fa-caret-down"></span>
					</button>
					and delete the median absolute deviation filter to show all rows.
				</p>

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Remove
					Dendrograms</a>
				<p class="collapse">Right-click on the column dendrogram and
					select "Delete". Do the same for the row dendrogram.</p>


				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Sort
					Rows</a>
				<p class="collapse">
					Click the MAD row annotation header in the heat map once to sort
					the heat map in ascending order by the median absolute deviation.
					Click it again to sort the heat map in descending order. Note that
					you can shift-click to sort multiple columns simultaneously.
					Alternatively, you can click
					<button title="Sort" name="sort" type="button"
						class="btn btn-default btn-xs">
						<span class="fa fa-sort-alpha-asc"></span>
					</button>
					to open a sort dialog.
				</p>

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Search
					Results To Top</a>
				<p class="collapse">
					Enter "BRAF" in the row search box. <br /> Click
					<button type="button" class="btn btn-default btn-xs">
						<i class="fa fa-level-up"></i>
					</button>
					to bring the matches to the top of the heat map.
				</p>



				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Visual
					Enrichment</a>
				<p class="collapse">

					Double-click on BRAF row to sort by dependency score. <br />
					Search columns for "skin". <br /> Do skin cell lines seem to be
					more dependent on BRAF than cell lines from other lineages? <br />
					You can optionally limit your search to within a field by typing
					the field name followed by a colon ":" and then the term you are
					looking for.

				</p>

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Nearest
					Neighbors</a>
				<p class="collapse">
					Click the tools icon
					<button type="button"
						class="btn btn-default btn-xs dropdown-toggle">
						<span class="fa fa-wrench"></span> <span class="fa fa-caret-down"></span>
					</button>
					and select "Nearest Neighbors". Click "OK" to run the analysis. <br />
					A new row annotation named "Pearson correlation" will appear. <br />
					What genes correlate with BRAF?
				</p>


				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Scatter
					Plot Matrix</a>
				<p class="collapse">
					Select the first three rows in order to select the top 3 most
					correlated genes with BRAF and all samples. Click the chart icon
					<button type="button" class="btn btn-default btn-xs">
						<span class="fa fa-line-chart"></span>
					</button>
					. Change the chart type to "row scatter" to assess the
					relationships between BRAF, FXR2, and ZNF781 simultaneously.
				</p>



				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Append
					Mutations</a>
				<p class="collapse">
					Click
					<button type="button" class="btn btn-default btn-xs">
						<span class="fa fa-folder-open-o"></span>
					</button>
					to bring up the file open window. <br /> Check "Append rows to
					current dataset" and select the file CCLE Mutations dataset. Change
					"Current dataset annotation name" and "New dataset annotation name"
					to "id" to match the ids in the existing dataset with the id in the
					mutational dataset. Scroll down to see the mutational data.
				</p>

				<!-- 				<a data-toggle="collapse" -->
				<!-- 					style="font-size: 1.2em; display: block; font-weight: 800;">Conditional -->
				<!-- 					Heat Map Color Schemes</a> -->
				<!-- 				<p class="collapse"> -->
				<!-- 					Select -->
				<!-- 					<button type="button" class="btn btn-default btn-xs"> -->
				<!-- 						<span class="fa fa-cog"></span> -->
				<!-- 					</button> -->
				<!-- 					to open the options window. <br /> Change "Color by" to "Source" <br /> -->
				<!-- 					Change "Color by value" to -->
				<!-- 					"CCLE_hybrid_capture1650_hg19_NoCommonSNPs_NoNeutralVariants_CDS_2012.05.07" -->
				<!-- 					<br /> Change "Predefined color schemes" to "MAF". -->
				<!-- 				</p> -->

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Toggle
					Mutation Visibility</a>
				<p class="collapse">
					Click
					<button title="Color Key" type="button"
						class="btn btn-default btn-xs" aria-expanded="false">
						<span class="fa fa-key"></span>
					</button>
					to open the color key. <br /> Click the "Synonymous" check box to
					visually hide synonymous mutations (note the matrix values are left
					unchanged).
				</p>

				<!-- 				<a data-toggle="collapse" -->
				<!-- 					style="font-size: 1.2em; display: block; font-weight: 800;">Group -->
				<!-- 					Rows</a> -->
				<!-- 				<p class="collapse"> -->
				<!-- 					Click -->
				<!-- 					<button title="Sort" name="sort" type="button" -->
				<!-- 						class="btn btn-default btn-xs"> -->
				<!-- 						<span class="fa fa-sort-alpha-asc"></span> -->
				<!-- 					</button> -->
				<!-- 					to open the sort and group by dialog. Sort by "Source". Next, -->
				<!-- 					select "Source" under the "Group by" field. Grouping adds -->
				<!-- 					whitespace between different values of the group by fields. -->
				<!-- 				</p> -->

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Annotate
					Selection</a>
				<p class="collapse">
					Enter "BRAF" in the row search box. <br /> Click
					<button type="button" class="btn btn-default btn-xs">
						<i class="fa fa-level-up"></i>
					</button>
					to bring the matches to the top of the heat map. Double-click to
					sort the heat map by the BRAF dependency score. Select the seven
					cell lines that have a dependency score less than or equal to -2.
					Right-click and select "Annotate Selection". Enter "BRAF_sensitive"
					for "Annotation name" and "y" for "Annotation value".
				</p>


				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">New
					Heat Map</a>
				<p class="collapse">
					Enter "CCLE" in the row search box to select the CCLE mutation
					data. <br />Right-click on the columns and select "Clear
					Selection" to clear the column selection. <br />Click the tools
					icon
					<button type="button"
						class="btn btn-default btn-xs dropdown-toggle">
						<span class="fa fa-wrench"></span> <span class="fa fa-caret-down"></span>
					</button>
					and select "New Heat Map". A new tab will open that contains the
					selected subset of the heat map.
				</p>

				<a data-toggle="collapse"
					style="font-size: 1.2em; display: block; font-weight: 800;">Fisher
					Exact Test</a>
				<p class="collapse">
					Click the tools icon
					<button type="button"
						class="btn btn-default btn-xs dropdown-toggle">
						<span class="fa fa-wrench"></span> <span class="fa fa-caret-down"></span>
					</button>
					and select "Marker Selection". Change "Metric" to "Fisher Exact
					Test". Change "Field" to "BRAF_sensitive". Set "Class a" to
					"BRAF_sensitive" and "Class b" to "". Set "Grouping value" to "4"
					to group missense, splice site, frame shift, and nonsense mutations
					together and no mutation, synonymous, in-frame indels, and other
					non-synonymous mutations together (Click
					<button title="Color Key" type="button"
						class="btn btn-default btn-xs" aria-expanded="false">
						<span class="fa fa-key"></span>
					</button>
					to see the numerical values used to encode mutation type). Click
					"OK" to run the analysis. <br /> A new row annotation named
					"Fisher Exact Test" will appear. <br /> What mutations distinguish
					BRAF sensitive cell lines from the other cell lines?
				</p>
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