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README.md

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@@ -15,50 +15,50 @@ This repository hosts the course material for the SIB course
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## Program
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Wednesday, May 27 |
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-----------------:|:-------------------------------------------------------
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9:00 - 9:30 | Welcome and setup of working environment (*C. Soneson*)<br>- Zoom<br>- slack workspace<br>- HackMD document<br>- Introducing participants (ice breaker)
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9:30 - 10:00 | Introduction to Renku (*R. Roskar*)
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10:00 - 10:30 | Introduction to the course (*M. Stadler*)<br>- Course overview, expected background<br>- Prepare renku workspace
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10:30 - 10:45 | *Break*
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10:45 - 11:15 | Combining the best of two worlds: Python + R (introduction, *M. Stadler*)
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11:15 - 11:30 | *Break*
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11:30 - 12:30 | Combining the best of two worlds: Python + R (interactive exercise, *M. Stadler*)
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12:30 - 13:30 | *Lunch*
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13:30 - 14:30 | Python + R (continued)
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14:30 - 14:45 | *Break*
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14:45 - 15:30 | Beyond cellranger: Quantification of gene expression (presentation, *A. Srivastava*)
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15:30 - 15:45 | *Break*
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15:45 - 16:45 | Quantification of gene expression (exercises, *A. Srivastava*)
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16:45 - 17:00 | *Break*
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17:00 - 18:00 | Quantification of gene expression (continued)
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| Wednesday, May 27 | |
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|------------------:|:-------------------------------------------------------|
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| 9:00 - 9:30 | Welcome and setup of working environment (*C. Soneson*)<ul><li>Zoom</li><li>slack workspace</li><li>HackMD document</li><li>Introducing participants (ice breaker)</li></ul> |
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| 9:30 - 10:00 | Introduction to Renku (*R. Roskar*) |
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| 10:00 - 10:30 | Introduction to the course (*M. Stadler*)<ul><li>Course overview, expected background</li><li>Prepare renku workspace</li></ul> |
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| 10:30 - 10:45 | *Break* |
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| 10:45 - 11:15 | Combining the best of two worlds: Python + R (introduction, *M. Stadler*) |
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| 11:15 - 11:30 | *Break* |
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| 11:30 - 12:30 | Combining the best of two worlds: Python + R (interactive exercise, *M. Stadler*) |
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| 12:30 - 13:30 | *Lunch* |
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| 13:30 - 14:30 | Python + R (continued) |
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| 14:30 - 14:45 | *Break* |
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| 14:45 - 15:30 | Beyond cellranger: Quantification of gene expression (presentation, *A. Srivastava*) |
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| 15:30 - 15:45 | *Break* |
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| 15:45 - 16:45 | Quantification of gene expression (exercises, *A. Srivastava*) |
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| 16:45 - 17:00 | *Break* |
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| 17:00 - 18:00 | Quantification of gene expression (continued) |
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Thursday, May 28 |
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-----------------:|:-------------------------------------------------------
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9:00 - 10:00 | RNA velocity (presentation, *C. Soneson*)
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10:00 - 10:15 | *Break*
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10:15 - 11:15 | RNA velocity (exercises, *C. Soneson*)
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11:15 - 11:30 | *Break*
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11:30 - 12:30 | RNA velocity (continued)
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12:30 - 14:00 | *Lunch*
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14:00 - 15:00 | Spatial transcriptomics (presentation, *A. Andersson*)
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15:00 - 15:15 | *Break*
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15:15 - 16:15 | Spatial transcriptomics (exercises, *A. Andersson*)
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16:15 - 16:30 | *Break*
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16:30 - 17:30 | Spatial transcriptomics (continued)
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| Thursday, May 28 | |
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| -----------------:|:-------------------------------------------------------|
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| 9:00 - 10:00 | RNA velocity (presentation, *C. Soneson*) |
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| 10:00 - 10:15 | *Break* |
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| 10:15 - 11:15 | RNA velocity (exercises, *C. Soneson*) |
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| 11:15 - 11:30 | *Break* |
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| 11:30 - 12:30 | RNA velocity (continued) |
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| 12:30 - 14:00 | *Lunch* |
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| 14:00 - 15:00 | Spatial transcriptomics (presentation, *A. Andersson*) |
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| 15:00 - 15:15 | *Break* |
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| 15:15 - 16:15 | Spatial transcriptomics (exercises, *A. Andersson*) |
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| 16:15 - 16:30 | *Break* |
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| 16:30 - 17:30 | Spatial transcriptomics (continued) |
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Friday, May 29 |
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-----------------:|:-------------------------------------------------------
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9:00 - 10:00 | Working with on-disk data formats (presentation, *M. Smith*)
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10:00 - 10:15 | *Break*
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10:15 - 11:15 | Working with on-disk data formats (exercises, *M. Smith*)
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11:15 - 11:30 | *Break*
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11:30 - 12:30 | Working with on-disk data formats (continued)
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12:30 - 13:30 | *Lunch*
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13:30 - 14:30 | Deep Generative Networks (presentation and exercises, *P. Papasaikas*)
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14:30 - 14:45 | *Break*
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14:45 - 15:45 | Deep Generative Networks (continued)
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15:45 - 16:00 | *Break*
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16:00 - 17:00 | Deep Generative Networks (continued)
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17:00 - 17:30 | Wrap-up (feedback form, slack workspace, all)
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| Friday, May 29 | |
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| -----------------:|:-------------------------------------------------------|
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| 9:00 - 10:00 | Working with on-disk data formats (presentation, *M. Smith*) |
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| 10:00 - 10:15 | *Break* |
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| 10:15 - 11:15 | Working with on-disk data formats (exercises, *M. Smith*) |
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| 11:15 - 11:30 | *Break* |
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| 11:30 - 12:30 | Working with on-disk data formats (continued) |
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| 12:30 - 13:30 | *Lunch* |
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| 13:30 - 14:30 | Deep Generative Networks (presentation and exercises, *P. Papasaikas*) |
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| 14:30 - 14:45 | *Break* |
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| 14:45 - 15:45 | Deep Generative Networks (continued) |
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| 15:45 - 16:00 | *Break* |
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| 16:00 - 17:00 | Deep Generative Networks (continued) |
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| 17:00 - 17:30 | Wrap-up (feedback form, slack workspace, all) |

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