aaronwolen

#!/usr/bin/env python3
"""
Download 10X Visium datasets using squidpy.

This tool wraps squidpy's internal visium() function to provide an easy way
to download and extract 10X Genomics Visium spatial transcriptomics datasets.
"""
from __future__ import annotations

import argparse

aaronwolen

aaronwolen

tiledbsoma.__version__        1.5.0rc0.post289.dev1706826235
TileDB-Py tiledb.version()    (0, 27, 1)
TileDB core version           2.21.1
libtiledbsoma version()       libtiledb=2.21.1
python version                3.11.8.final.0
OS version                    Darwin 23.3.0


Checking tiledb...

aaronwolen

#! /usr/bin/env Rscript

library(tiledb)
library(data.table)
library(nycflights13)

TILEDB_URI <- file.path(tempdir(), "tiledb-flights")
if (dir.exists(TILEDB_URI)) unlink(TILEDB_URI, recursive = TRUE)

STATS_DIR <- file.path(getwd(), "stats")

aaronwolen

Quokka Filters

aaronwolen

TileDB Dense Array Queries

Setup

Create a dense matrix random integers.

library(tiledb)
set.seed(123)

aaronwolen

#!/usr/bin/env Rscript
library(docopt)

# Changelog
# ---------
# 0.1.1: Consolidate fragment metadata and commits after ingestion
# 0.1.0: Initial release

# docopt ------------------------------------------------------------------

aaronwolen

README

Setup

Use conda to install the TileDB Python API and other dependencies.

mamba env create -f environment.yaml
conda activate aind-demo

aaronwolen

Our starting point is raw counts in a sparse matrix, smat (4 genes, 5 cells):

   c1 c2 c3 c4 c5
g1  8  .  .  .  5
g2  .  5  7  .  .
g3  1  .  .  5  .
g4  8  .  .  7  .

aaronwolen

13,15c13,17
<       dtype=object)), ('real_start_pos', array([43338668, 43341403, 43341867, 43342848, 43342933, 43345733,
<        43346403, 43349192, 43350860, 43351009], dtype=uint32)), ('end_pos', array([43338668, 43341403, 43341867, 43342848, 43342934, 43345733,
<        43346403, 43349192, 43350860, 43351019], dtype=uint32)), ('qual', array([ 49.71,  50.  ,  50.  ,  50.  ,  50.  ,  49.27,  49.57,  46.14,
---
>       dtype=object)), ('real_start_pos', array([ 393434177, 2913177362, 3658721541, 2359512986, 4034073792,
>        2945374281, 1320880414, 2723889732, 1316948380, 1664381440],
>       dtype=uint32)), ('end_pos', array([ 393434177, 2913177168, 3658721541, 2359496344, 4034073792,
>        2408503627, 1320880152, 2723889732, 1325336600, 1664381440],
>       dtype=uint32)), ('qual', array([ 49.71,  50.  ,  50.  ,  50.  ,  50.  ,  49.27,  49.57,  46.14,