https://trovomics.com/tutorials daily 0.75 2026-01-20 https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/4fab497c-c298-45af-826a-d08a4b7e01e8/Trovomics+Gray+Logo.png https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/4fab497c-c298-45af-826a-d08a4b7e01e8/Trovomics+Gray+Logo.png https://trovomics.com/tutorials/go monthly 0.5 2024-03-15 https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/a16b9836-eac3-48ab-9d6d-1f3612c3bec9/2024-2-16+settings.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 1. Overview of the left-hand menu. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/c1c71c9f-3a00-4da5-a692-6582df46a016/GO+plot+elements.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 2. Overview of the main elements in a GO plot in Trovomics. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/afd390bd-2843-49fe-a7e5-cf613f2a3d30/GO+hover.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 3. The cursor is hovered over a bar that represents the GO term ‘extracellular matrix organization’, and revealed a text box that contains more information on this term. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/df05fc83-3318-4df0-8490-8563c32800db/GO+term+count.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 4. The number of GO terms shown for each GO category were changed (arrows). https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/3263e09e-599e-4b7b-b0cd-d4757c89377f/GO+filter+term.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 5. They keyword ‘neuro’ is entered in Keyword Search (arrow), so only GO terms with the keyword ‘neuro’ are shown on the plot. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/e3e40aca-f4f3-4c91-98f4-52c067f15ab7/GO+colorsort.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 6. ‘P value’ is selected under Color/Sort By (box). Therefore, the bars on the GO bar graph are colored to represent P values according to the color scale. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/44efa91a-048f-4535-86c5-a2befa3dbbf2/GO+color+scale.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 7. Under Color Scale, ‘Viridis’ is selected as the color scale. This changes the color scale to a yellow-green-purple gradient. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/739d844a-7b34-445f-8e62-1f12ae6c6df4/GO+reverse+color.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 8. The color scale is reversed, now yellow represents lower P values and purple represents higher P values. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/53f85e31-61ec-4db4-bd00-f3c204046867/GO+save+genelist.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 9. The GO term ‘neurotransitter transport’ is selected in the Data Table. The 22 genes in the term are saved to a new gene list. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/cf11b618-2b11-44f4-a3f1-91988f1da181/GO+plot+title.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 10. The plot title and font size has changed to ‘GO Plot - Neuro terms’ and ‘27’, respectively. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/48fe15c7-21e6-49a5-a69f-59c1d6aa2d75/GO+height+and+width.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 11. The plot dimensions is changed by the settings in Plot layout. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/b856fdcc-6eed-4589-bfc3-78ac3b3acd19/GO+all+downloads.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 12. GO plot methods and data can be downloaded within All Downloads. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/416404f8-67b0-424c-8102-a439f4d847d8/GO+methods.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 13. Sample GO Methods .TXT file. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/8f799fec-f1cb-4f82-b4d2-a7747df9c109/GO+save+plot.png RNA-Seq Tutorials - Visualizer: GO (Gene Ontology) - Make it stand out Image 14. The arrow is pointing to the download icon. The plot is being downloaded as a JPEG image. https://trovomics.com/tutorials/volcano monthly 0.5 2024-03-15 https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/6445f337-964e-416c-8ed3-ed0dc3263eaa/2024-2-16+settings.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 1. Overview of the left-hand menu. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/4f8f5ee8-6383-421e-acf4-5e05aad3c490/2024-2-6+select+a+comparison1.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 2. A comparison must be selected before visualizing the volcano plot. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/8faf402a-1432-4b38-8dc8-7dc7ca088802/2024-2-16+volcano+components.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 3. Overview of the main elements in a volcano plot in Trovomics. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/61b64075-40ad-4bbd-8d97-e11de540334c/2024-2-16+p+value1.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 4. Significance is shown through P values as opposed to adjusted P values (the default) on the Y axis. The cutoff value is represented by the position of the black, horizontal dashed line on the Y axis. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/cf7bb873-1161-4d7f-826b-815c2f1e6ef5/2024-2-20+remove+group1.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 5. All “Upregulated” genes were removed from the plot (dashed box), evidenced by the label being grayed out (arrow) https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/25b8c86e-3725-4d36-9476-af0781fbfeae/2024-2-20+show+one+group1.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 6. Only “Downregulated” genes are shown on the plot (arrow), evidenced by all other groups being grayed out. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/6dc31d47-13b9-40a3-b382-f46cabc9dc95/2024-2-20+hover1.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 8. The cursor is hovered over a point that represents COL20A1, and revealed a text box that contains information about the gene name, comparison, average count, Log2FoldChange, FoldChange, P value and source. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/abfdfe54-ded9-4790-b129-d476ea314526/2024-2-20+fold+change1.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 9. The fold change was set to “4.3” (box) under FC Cut Size, which translates to a Log2FoldChange of 2.1. The FC Cut Size value is represented by position of the two black, vertical dashed lines on the volcano plots that are visible at -2.1 and +2.1 on the X axis (arrows). https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/adc6ef81-7891-4a67-84c3-3c52076e273b/2024-2-20+Y+max1.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 10. The max value for the Y axis was set to “100” under Y Max Size (box), resulting in the “-log10(pvalue)” on the Y axis to go up to 100. All genes have a value below 100 and therefore no points were represented as triangles in this example. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/bf0ba0c2-88f0-4bdb-b6a6-cef64f924f46/2024-2-20+zoom.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 11. A section of the volcano plot was zoomed in on. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/2783967e-b600-4469-a4c1-a9e289f35da0/tools1.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 12. The Lasso Select Tool and the Square Select Tool are found at the top of left corner of the plot. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/1940a773-1594-451b-9718-abcce6728ded/2024-2-20+mark+size1.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 13. The point size was set to “8” on the slider bar under Mark size (box), which increased the size of all points on the plot. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/373d2f6e-ba6a-4cda-a4a5-2c36bc19fbab/2024-2-20+point+colors.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 14. Colors for each group were selected using the associated color pickers (box). https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/17592ae7-294c-4786-822f-9308514e8f88/2024-2-20+plot+title.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 15. The plot title and font size has changed to ‘Volcano Plot Tutorial’ and ‘17’, respectively. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/63eb445a-2c84-49ea-ad01-824d043469df/2024-2-20+plot+width+height.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 16. The plot is enlarged by increasing the width and height. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/e89f07f5-c81c-44c6-b719-f1be74f1aae7/2024-2-20+downloads.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 17. Volcano plot methods and data can be downloaded within All Downloads. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/4ee6b3ef-8fb0-4856-9cad-15c358373b57/vol+methods.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 18. Sample Volcano Methods .TXT file. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/764c8547-3de5-43f6-8891-c8ddab60b3e3/2024-2-20+plot+download.png RNA-Seq Tutorials - Visualizer: Volcano Plot - Make it stand out Image 19. The arrow is pointing to the download icon. The plot is being downloaded as a JPEG image. https://trovomics.com/tutorials/how-to-create-a-metadata-table monthly 0.5 2024-02-23 https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/2d969824-8799-4b84-8cca-f8b5f8ef6013/2024-2-6+Download+table+Trovomics.png RNA-Seq Tutorials - How to create a metadata table - Make it stand out Image 1. Click the icon (arrow) to download the metadata table template at the Build Your Experiment step in Create Experiment. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/9f616554-4ba8-4ea4-bcb8-4dea533dda75/2024-2-6+sample.png RNA-Seq Tutorials - How to create a metadata table - Make it stand out Image 2. Trovomics’s metadata table template. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/84b23641-4ea3-4a2f-a8f8-ecb23a0a6d7b/2024-2-6+pairedend+and+single+end+sample+names.png RNA-Seq Tutorials - How to create a metadata table - Make it stand out Image 3. Single-end sequencing read types will only have one FASTQ file per sample (left). Paired-end types will have two FASTQ files per sample (right). Duplicate the your sample name in another row to accommodate another FASTQ file name. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/a6a96f18-82dd-4402-9831-53420b66710f/2024-2-6+insert+columns.png RNA-Seq Tutorials - How to create a metadata table - Make it stand out Image 4. Insert columns in the table to add more experimental values to your metadata. Rename the default “Disease”, “Age”, and “Organism” columns as necessary, or delete if not needed. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/ed36e476-d90d-47d2-be0a-e726b91ea5d0/2024-1-26+completed.png RNA-Seq Tutorials - How to create a metadata table - Make it stand out Image 5. An example of a completed metadata table for Trovomics. https://trovomics.com/tutorials/create-experiment-tutorial monthly 0.5 2025-05-27 https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/f758336d-2923-4f73-8462-0181a016326f/2024-1-25+Experiments+Dashboard+Trovomics+300dpi.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 1. Experiment dashboard in Trovomics with an arrow pointing to the Create Experiment button. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/4c2e334d-aabd-4c64-938d-3fa394971e9e/2024-1-25+Batch+effects+warning.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 2. The batch effects warning pop-up that appears after you click Create Experiment. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/33392d43-a83c-4109-89d2-51467ea43d95/2024-1-25+Enter+experiment+details.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 3. The Enter Experiment Details step in Create New Experiment. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/277222ec-1627-4ffe-81df-532d9dff7a07/2024-1-25+Enter+sequencing+details.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 4. The Enter Sequencing Details step in Create New Experiment. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/5a9608cf-2343-4bc9-a6e1-2ae0b0c2473c/2024-1-25+Format+your+experimental+design+metadata+table.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 5. Format Your Experimental Design section in the Build You Experiment step. A metadata table has been attached “YN NP PP upload table.csv”. Arrows designate where you click to upload a file (left) and delete a file (right). https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/b536e494-b4bd-488f-935a-57504c67c1f2/2024-1-26+uploading+files.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 6. Upload Your Sample Files section in the Build You Experiment step with an arrow pointing where to click to upload files. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/f88dba72-1d76-4af4-98ab-c247ed3a72aa/2024-1-25+uploading+files+progress.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 7. You can monitor file upload progress in the pop-up (top and middle panels). Once files are done uploading, you will be automatically directed to the Edit Samples step (bottom panel) https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/59e1d375-da16-4721-b2d2-060dee765f67/2024-1-25+edit+samples.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 9. Review Your Variables and Values section in the Edit Samples step. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/2735c1a3-4f96-4905-bf74-0a5bb3fead74/2024-1-26+review+your+individual+samples.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 10. Review Your Individual Samples section in the Edit Samples step. Arrows are pointing to where you click to add an additional sample (top left), delete a sample (right), and view sequencing files associated with each sample (bottom left). Use the search bar to find samples by their Sample Name (middle). https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/e909688d-ef65-4650-ae0c-83fd726a8c80/2024-1-26+add+sample.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 11. Adding a new sample called “NP+ANG4_NEW” in Review Your Individual Samples. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/20ba80b6-12ab-44e1-946f-ed9006d4383f/2024-1-26+duplicate+sample.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 12. Selecting a sample to duplicate, will duplicate the sample’s details (name, experimental variables and values). Sequencing files are not duplicated and will need to be uploaded separately, similar to adding a new sample. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/156a2dd1-527b-43ae-8f36-5b35294d3439/2024-1-26+edit+sample+metadata.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 13. Steps involved in updating sample experimental variables or values. Changes to experimental variables and values are made in the Review Your Variables and Values section. Once completed, changes can be reviewed in Review Your Individual Samples. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/66dbe051-6376-43ac-9491-0fa07a840cd7/2024-1-26+edit+sample+name.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 14. Directly edit sample names under the Sample Name column. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/cd8e4239-5a81-416a-9917-2682172f8b2b/2024-1-26+assign+new+value.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 15. Assigned the incorrect experimental value on your metadata table? No problem, you can select from the available options using the drop-down menus. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/babf5400-8940-4589-88d0-3dc78a716cc4/2024-1-26+edit+file+metadata.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 16. Edit file metadata associated with a sample. Changing file metadata is not recommended in most instances. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/41d828e5-c74f-4166-8f37-f7a0ee5cb0d0/2024-1-25+Review+and+create.png RNA-Seq Tutorials - Create an experiment in Trovomics - Make it stand out Image 17. Review & Create step within Create New Experiment with an arrow pointing to where you can click to edit details in a section. https://trovomics.com/tutorials/category/App monthly 0.5 https://trovomics.com/tutorials/category/VISUALIZATION monthly 0.5 https://trovomics.com/tutorials/category/Tutorial monthly 0.5 https://trovomics.com/tutorials/category/FILTERING monthly 0.5 https://trovomics.com/tutorials/category/PRODUCT monthly 0.5 https://trovomics.com/tutorials/tag/Tutorial monthly 0.5 https://trovomics.com/tutorials/tag/RNASeq monthly 0.5 https://trovomics.com/resources daily 0.75 2026-01-19 https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/4fab497c-c298-45af-826a-d08a4b7e01e8/Trovomics+Gray+Logo.png https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/4fab497c-c298-45af-826a-d08a4b7e01e8/Trovomics+Gray+Logo.png https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/4d5759d8-356f-4e66-8927-a1471889fab8/Screen+Shot+2023-10-27+at+2.08.19+PM.png https://trovomics.com/resources/precision-medicine-with-dr-brian-mcdonough monthly 0.5 2025-02-04 https://trovomics.com/resources/compression-using-genesqueeze monthly 0.5 2025-01-27 https://trovomics.com/resources/what-is-rna-sequencing-and-what-does-it-tell-us monthly 0.5 2024-05-08 https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/b8a521c5-94b4-4542-b4f6-96f3fb88dd90/Picture1.png Resources - What is RNA-Sequencing, and what does it tell us? - Make it stand out A schematic representation of the RNA-Seq protocol. (2) https://trovomics.com/resources/timing-trovomics monthly 0.5 2024-03-13 https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/3cff2ac0-924a-43db-b95a-8e5ca7aa960d/unlock.png Resources - How long does RNA-Seq analysis take in Trovomics? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/8737b930-0e2b-44b9-a761-9e0195df9bad/time+breakdown1.png Resources - How long does RNA-Seq analysis take in Trovomics? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://trovomics.com/resources/what-is-a-metadata-table-for-rna-seq-data-and-why-is-it-important monthly 0.5 2024-02-21 https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/5d27f604-2093-42c3-aeae-b2488a41c65a/types+of+metadata+table.png Resources - What is a metadata table for RNA-Seq data? And why is it important? - Make it stand out Types of metadata according to FAIR and Sabot et al. (1,2) https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/5d50b0ba-f41e-460a-9809-2564d7d97109/openaccesspublications1.png Resources - What is a metadata table for RNA-Seq data? And why is it important? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/82c1e8c5-48a7-4b33-b033-90804d9d8bf1/using+metadata-linkedin2.png Resources - What is a metadata table for RNA-Seq data? And why is it important? - Make it stand out Simplified illustration of how metadata impacts RNA-Seq analysis and visualization. https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/257b8749-3a0c-4e3b-a47a-7480db487247/ncbigeosample.png Resources - What is a metadata table for RNA-Seq data? And why is it important? - Make it stand out NCBI GEO’s metadata table template https://images.squarespace-cdn.com/content/v1/65021da80da86e3a2f803d7a/616bf34b-4df3-493c-8103-f856247731d8/2024-1-26+completed.png Resources - What is a metadata table for RNA-Seq data? 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