GTEx analysis seems to be broken

BioJupies

Automated generation of Jupyter Notebooks for RNA-seq data analysis via user interface (http://biojupies.cloud).

Source code for the RNA-seq analysis plugins available at https://github.com/MaayanLab/biojupies-plugins.

Overview

What is BioJupies?
How can I generate notebooks using BioJupies?
How can I upload my own RNA-seq data to BioJupies?
What analyses can BioJupies perform?
Can I contribute my RNA-seq analysis tools?
How can I download and rerun my notebooks?
References

What is BioJupies?

BioJupies is a web server which allows users to automatically generate Jupyter Notebooks from RNA-seq datasets through an intuitive interface, with no knowledge of coding required. It can be accessed for free from http://biojupies.cloud.

How can I generate a notebook using BioJupies?

Generating a notebook using BioJupies requires three steps:

First, select an RNA-seq dataset you with to analyze. You can upload FASTQ files, gene expression tables, or use a search engine to browse over 6,000 public datasets published in the Gene Expression Omnibus and processed by ARCHS4.
Second, add one or more computational tools to analyze the data. BioJupies currently supports 14 plugins to perform exploratory data analysis, differential gene expression, enrichment analysis, and small molecule queries.
Third, generate the notebook with the desired settings. The notebook will be served to you through a URL, and can be easily downloaded and rerun on your local computer.

How can I upload my RNA-seq data to BioJupies?

Users can upload their RNA-seq datasets for analysis at https://amp.pharm.mssm.edu/biojupies/upload.

BioJupies currently supports uploading RNA-seq datasets in the FASTQ format or tables of gene-level counts.

Note: While the user may successfully generate a notebook from normalized gene expression counts or microarray data tables, the tools are NOT yet optimized to handle such data. Such results should be interpreted with caution.

The Enrichment Analysis and Small Molecule Query plugins currently support datasets uploaded with gene symbols as row identifiers. When uploading datasets with different identifiers (e.g. ENSEMBL IDs, Entrez IDs), please note that these plugins may return empty results.

What analyses can BioJupies perform?

BioJupies currently provides 14 RNA-seq data analysis plugins, divided into four categories. For more information about the plugins, visit https://github.com/MaayanLab/biojupies-plugins.

Can I contribute my RNA-seq analysis tools?

Developers are welcome to contribute their own RNA-seq data analysis plugins for integration in BioJupies. Once integrated, the plugin will be made available to all users for notebook generation and published on the BioJupies plugins GitHub repository.

To contribute your plug-in, please visit https://amp.pharm.mssm.edu/biojupies/contribute.

How can I download and rerun my notebooks?

After generating a notebook, users can download and execute it locally using the maayanlab/biojupies-notebooks Docker container.

To do this, the following steps are required:

Pull the latest version of the Docker container from the console:

docker pull maayanlab/biojupies-notebooks

Identify the notebook's unique ID (a 9-character alphanumeric string) from its URL - e.g. 5DAHiejHN.

Launch the Docker container.

docker run -it -p 8888:8888 -e NOTEBOOK_UID=5DAHiejHN maayanlab/biojupies-notebooks

Note: replace 5DAHiejHN with the UID of the notebook you wish to rerun.

Access the local Jupyter Notebook server from your browser at port 8888.

Execute and customize your notebook from the Jupyter server.

For more information about reusing notebooks, see https://amp.pharm.mssm.edu/biojupies/docker.

References

BioJupies is available as a pre-print on BioRxiv: BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud Torre, D., Lachmann, A., and Ma’ayan, A. (Cell Systems, 2018)

License

This project is licensed under the Apache-2.0 License - see the LICENSE.md file for details

	function upload_reads() {

	// Get credentials
	username = 'biojupies';
	passwd = 'sequencing';

	// Get files
	var files = $('#fileinput').prop('files');

	// Loop through files
	$.each(files, function(index, file) {

	// Add progress bar
	progress_bar(file['name']);

	// Get Sign Policy
	$.getJSON("https://amp.pharm.mssm.edu/charon/signpolicy?username=" + username + "&password=" + passwd, function (data) {

	// Create Form
	var FD = new FormData();
	FD.append('key', data['uid'] + "/{{upload_uid}}-${filename}");
	FD.append('AWSAccessKeyId', data['cid']);
	FD.append('acl', 'private');
	FD.append('success_action_redirect', 'success.html');
	FD.append('policy', data['policy']);
	FD.append('signature', data['signature']);
	FD.append('Content-Type', 'application/octet-stream');
	FD.append('file', file);

	// Get filename
	var filename = file['name'];

	// Create Request
	var xhr = new XMLHttpRequest();
	xhr.open("POST", "https://" + data["bucket"] + ".s3.amazonaws.com/", true);
	xhr.onloadstart = function (e) {
	console.log("start")
	}
	xhr.onloadend = function (e) {
	// Set complete status on progress bar
	$('[data-filename="' + filename + '"] .progress-bar').attr('data-status', 'complete');
	$('[data-filename="' + filename + '"] .progress-bar-text span:first-child').html('Successfully uploaded ');
	$('[data-filename="' + filename + '"] .progress-bar-text span:last-child').html('');

	// Activate button if all progress bars are complete
	if ($('.progress-bar').length === $('.progress-bar[data-status="complete"]').length) {
	$('[form="read-upload-form"]').prop('disabled', false).toggleClass('black white bg-white bg-blue');
	}
	console.log("end")

	// Call FASTQ Upload Status API
	}
	xhr.upload.addEventListener('progress', function (evt) {
	if (evt.lengthComputable) {
	var progress = Math.ceil((evt.loaded / evt.total) * 100)+'%';
	$('[data-filename="' + filename + '"] .progress-bar').html(progress);
	$('[data-filename="' + filename + '"] .progress-bar').css('width', progress);
	}
	}, false);
	xhr.send(FD);

	});

	})
	}

	dropzone = $("#dropzone").dropzone({
	dictDefaultMessage: "Drag and drop your file here, or click to browse and upload it.",
	url: "{{ url_for('upload_dataframe_api') }}",
	success: function(file, response){

	// Parse response
	response = JSON.parse(response);

	// Add dataset
	addTable(response);

	}
	});

	$(document).ready(function () {

	// Load GTEx metadata
	$.ajax({
	url: "{{ url_for('gtex_api') }}",
	dataType: "json",
	method: "POST",
	success: function(json) {

	// Loop through tables
	$('.gtex-table').each(function(index, elem) {

	// Create table
	var table = $(elem).DataTable({
	data: json,
	aaSorting: [],
	pagingType: 'simple',
	columns: [
	{data: 'checkbox', orderable: false, className: 'select-checkbox'},
	{data: 'Age', orderable: false},
	{data: 'Gender', orderable: false},
	{data: 'Tissue', orderable: false}
	],
	select: {
	style: 'multi'
	},
	fnCreatedRow: function (nRow, aData, iDataIndex) {
	$(nRow).attr('data-sampleid', aData['id']); // or whatever you choose to set as the id
	},
	initComplete: function () {
	this.api().columns().every(function () {
	var column = this;
	if (column.index() > 0)
	{
	var select = $('<select class="gtex-sample-filter"><option value=""></option></select>')
	.appendTo($(column.header()).empty())
	.on('change', function () {
	var val = $.fn.dataTable.util.escapeRegex(
	$(this).val()
	);

	column
	.search(val ? '^' + val + '$' : '', true, false)
	.draw();
	});

	column.data().unique().sort().each(function (d, j) {
	select.append('<option value="' + d + '">' + d + '</option>')
	});
	}
	});
	}
	})

	// Add listener for checkbox
	table.on('click', '.select-all', function(evt) {

	// Get button
	var $button = $(this);
	// Deselect and select
	if (table.rows({ selected: true }).count() > 0) {
	table.rows().deselect();
	$button.removeClass('active');
	} else if (table.rows({ filter: 'applied' }).count() == table.rows().count()) {
	alert('Please select at least one filter in the table such as age, gender or tissue.')
	} else {
	table.rows({ filter: 'applied' }).select();
	$button.addClass('active');
	}

	})

	// Add update number of samples
	table.on('select deselect', function(evt) {
	var $col = $(evt.target).parents('.gtex-table-col'),
	selected_rows = table.rows({ selected: true }),
	ids = Array.from(selected_rows.data().pluck('id'));

	// Update number
	$col.find('.gtex-table-header .nr-samples').html(selected_rows.count());

	// Add samples to HTML
	// $col.find('.selected-samples').data('id', ids);
	$col.find('.selected-samples').val(ids);

	})


	// Change group names
	table.on('change', '.gtex-sample-filter', function (evt) {
	var $table = $(this).parents('table'),
	group_name = $table.find('.gtex-sample-filter').map(function () { if ($(this).val().length) {return $(this).val()} }).get().reverse().join(', ');
	$table.parents('.gtex-table-col').find('.gtex-group-name').first().val(group_name);
	console.log(group_name);

	})

	})

	// Show table
	$('.gtex-table').removeClass('d-none');
	$('.gtex-table-header').removeClass('d-none');
	$('.gtex-loader').addClass('d-none');

	}
	})

	// Check sample size
	$('button[form="select-samples-form"]').click(function(evt) {

	// Prevent submission
	evt.preventDefault();

	// Get group size
	group_1_size = $('#DataTables_Table_0_wrapper tr.selected').length;
	group_2_size = $('#DataTables_Table_1_wrapper tr.selected').length;

	// Check sizes
	if ((group_1_size < 2) \|\| (group_2_size < 2)) {

	// Alert
	alert('Please select at least two samples for each group using the provided checkboxes.')

	} else {

	// Submit
	$('#select-samples-form').submit();

	}
	})

	})

maayanlab / biojupies Goto Github PK

biojupies's Introduction

BioJupies

Overview

What is BioJupies?

How can I generate a notebook using BioJupies?

How can I upload my RNA-seq data to BioJupies?

What analyses can BioJupies perform?

Can I contribute my RNA-seq analysis tools?

How can I download and rerun my notebooks?

References

License

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