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I want to count points (1000 of students home) in district polygons with Qgis 2.16. I didn't find the tool in the analysis tools plugin.

Is there another plugin or method I could use to perform this task ?

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The tool you're looking for is now called "Count points in polygons", and it can be found in the QGIS's Processing Toolbox (Ctrl+Alt+T) under Vector analysis tools or can be also launched found in Vector > Analysis Tools > Count Points in Polygons.

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