Wally visualizations
This Capsule creates a genomic alignment plot of reads in a specified region mapped to a reference. The visualization of genomic alignments was heavily inspired by IGV, and customized to visualize structural variation and CNVs.
Genome .fasta reference and .fai file
.bam files
Samplot Visualization (from coordinates)
This Capsule is a command line tool for rapid, multi-sample structural variant visualization.
compare sheet
.bam files
Dose response
This Capsule produces dose response curves that describe the magnitude of the response as a function of exposure (dose) to a condition after a certain exposure time.
.csv file containing gene expression and treatment dosage (see README for details)
DESeq2
This Capsule performs differential gene expression analysis with potential input types: 1. Transcript abundance; 2. Counts data; 3. HTseq-counts data; 4. Summarized experiment in RDS format.
Input varies depending on the source (i.e., Seurat vs RSEM) see README for details.
Mol* Viewer for PDB Files
This Capsule allows you to view PDB files interactively on a Streamlit cloud workstation using the Mol* 3D Viewer.
Protein structure files in .pdb format
TensorBoard GPU
This Capsules allows users to view model experiment metrics like loss and accuracy, visualizing the model graph, project embeddings to a lower dimensional space and more. This capsule shows an example from the Tensorboard website.
This Capsule runs on GPU instances and comes preloaded with Tensorflow.
None
RShiny Cell
ShinyCell is an R package that allows users to create interactive Shiny-based web applications to visualize single-cell data.
Single cell .rds inputs from Seurat (see README)
1-3. Single Cell Analysis Tutorial (Scanpy & Seurat)
Tutorials to describe working with Single Cell data for Scanpy and Seurat:
1. Preprocessing and clustering 3k PBMCs
2. Core Plotting Functions
3. How to preprocess UMI count data with analytic Pearson residuals
Tutorial datasets (see README for details)
5-6. Single Cell Analysis Tutorial (Scanpy)
Tutorials demonstrating how to regress cell cycle effect and how to simulate data using a literature-curated boolean gene regulatory network.
Tutorial datasets (see README for details)
7-10. Single Cell Analysis Tutorial (Scanpy) Advanced
Tutorials for advanced Single Cell processing.
Tutorial datasets (see README for details)
MLflow Orchestrator Capsule
This is a central MLflow "Orchestrator" capsule that can be used to interactively view the results from multiple machine learning capsules using the same MLflow database.
None
