New ERGO Feature: Bulk Downloads

You’ve requested and we’ve delivered! ERGO now has fast bulk downloads from projects and workflows. For the moment this feature is only available on up-to-date chromium browsers such as Google Chrome or Microsoft Edge.

Here is how it works, first on any project or workflow, click on the “Download … Files” button.

This will add all of those files to the download queue. Each file can be removed from the queue by clicking the toggle on the left.

Clicking on “Start Download” starts the download from ERGO using the number of simultaneous downloads you’ve selected. You can stop your download at any time by clicking “Stop Download”. Click “Start Download” will start the download where you left off.

Transferring files can also be managed using our API. Please enquire to learn more about this feature, ERGO’s API, or any other questions.

ERGO Updates

Igenbio’s developers have spent this summer creating many ‘quality of life’ improvements to ERGO’s user interfaces. Today I’ll highlight a few changes:

New color palette options available under chart customizations

• General Changes

  • Most charts now support four new color modes, including two that are colorblind friendly palettes, such as the default color scheme.

  • Color palettes can be selected from the “Customize” menu below the chart.

In Expression Analysis:

• More detail in error dialogs. For example, when you are running a DESeq2 analysis, if there is a problem (not enough replicates) you’ll get a more detailed message that could aid you in correcting the issue.

• Changed the truncation of long titles. Now the analysis tab will auto expand to display the entire title. This will make it easier to differentiate between open analysises.

• When creating new analysis, there is now an option to add/remove samples or conditions. This will allow you to quickly create customized analysis.

Easily remove conditions and samples to create the custom analysis that you want

• Differential Analysis

  • New Column: ‘Category’. This contains all of the categories at the current ontological level that this feature belongs to.

  • Hovering over a row in the DEG table highlights the categories (or feature in Volcano plot) in the chart that the feature belongs to.

  • New table options to set the precision and number display preferences for fold change, p-value, q-value, and others.

  • More meta feature data is now indexed when searching the table, including KEGG, COG, Pfam, and pathways.

  • New option to sort the plot by value (smallest to largest)

  • New plot options, such as Min Fold Change, Max Fold Change, Median Fold Change, Count (of genes), Mean -log10 p-value, Mean -log10 q-value. This will enable you to quickly identify which category has the most significance.

  • New option option to plot two different series - on for all changes that have positive fold change and another for those with negative fold change. This will make it more obvious of the apparent direction of the category as a whole as averaging the fold change had the effect of making the category look as though at no change at all.

  • New filter option for filtering by absolute value of fold change. This way you can filter the table (and subsequent plots) by features with a fold change in either direction.

  • New “Bar” plot.

• Gene Set Enrichment Analysis (GSEA)

  • Added condition toggle for heatmaps. Under “More Chart Options” there is an option to quickly toggle on/off a condition to be displayed on the heatmap.

  • KEGG Analysis results can now be projected onto KEGG Pathways.

Demonstration of new plot option to have two separate series - one representing the mean fold change of all positive fold changes and another representing the mean of all negative fold changes.

• In Read QC Analysis

  • Added details of over-represented sequences, which could be an indication of adapters or other sequences that need to be filtered

  • Some speed improvements

New ERGO Feature: GFF Visualization

ERGO now supports viewing GFF (Generic Feature Format) files in the Genome Browser. ERGO previously supported importing GFF3 and GTF as new genomes for licensees of ERGO Enterprise Edition.

You can now drag and drop your GFF files directly into ERGO. ERGO then sorts and indexes your GFF file for quick access. After you associate the GFF file with your genome of choice, you will be able to add the GFF file as a new track in the Genome Browser.

Adding a GFF File to ERGO

1. Log into ERGO, then click the upload icon on the top toolbar. This will reveal your current uploads. Drag and drop your GFF file into the box or click on the “+” icon to browse and select your files. Multiple files are accepted.

2. After your file has uploaded, click on the box next to the name to edit the file. If your file does not end in “.gff” you may need to change the “Type” to “gff - Genome Feature Format Version 3 (gff)”. Click on “+Genome” to select a genome for this GFF file.

Viewing GFF Files in ERGO

After your GFF has been uploaded and the file type and genome has been set, you can view it on ERGO’s Genome Browser. The GFF file will appear when your click on “>Tracks” on the Genome Browser for the selected genome.

New ERGO Feature: Affected Features for Variants

When you add annotated BCF or VCF files to ERGO, it automatically computes variant metrics, including the features that have been affected. Easily find which genomic features are affected by variation by clicking on the “Affected Features” tab. From here you can search for your feature or function of interest and see which features have been affected. Clicking on the arrow reveals more information about the feature, including which pathways it is in and which variants have affected this feature.

New ERGO Feature: Variant Filtering

Hey ERGO users! You can now filter through the large lists of variants according to their fields and focus in on the ones that are most important. The variant filtering feature can be found under the “Variant List” tab in the variant analysis workflow. By simply clicking on “Add Filter”, located next to “Settings”, you can choose your filter(s) and focus in on specific contigs, frame shifts, specific annotations and attributes, and much more.

Igenbio Provides Automated Variant Analysis

CHICAGO--(BUSINESS WIRE)--Igenbio, Inc. announced today the expansion of variant analysis service offerings. Igenbio’s comprehensive variant analysis service answers pressing questions in genome differences reflecting changes to metabolic pathways and genetic associations relevant to disease- or cancer-causing variations. Igenbio’s flagship product ERGO 2.0 enables researchers to deepen the analysis of variations with interactive visualizations enabling industrial, academic, and medical scientists to rapidly uncover hidden genetic variations and develop diagnostic biomarkers.

“Research scientists can use ERGO’s Variant workflow by simply “dragging-and-dropping” the sequence files into ERGO and receiving scientifically rigorous results in minutes. Discover single nucleotide polymorphisms (SNPs), insertions, deletions (INDELS), along with their functional relevance and deleterious effects. ERGO does it all for you: from sequence quality assessments to annotating variant effects of any genome. This furthers our goal of making the best bioinformatics analysis available to all researchers, regardless of their computer experience.”, says Benjamin Vaisvil, VP, Bioinformatics and Software Development at Igenbio, Inc.

About Igenbio

Chicago-based Igenbio, Inc. specializes in research in genomics, bioinformatics, and transcriptomics. Igenbio, Inc. serves a broad customer base across industry, academic and government institutions. ERGO 2.0 integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, with tools and workflows for common bioinformatics tasks. Our goal is to make the best scientific analysis available to all researchers.