README.md
In Bioconductor/HCABrowser: Browse the Human Cell Atlas data portal

The Human Cell Atlas (https://www.humancellatlas.org/) was created in order to create comprehensive reference maps of all human cells as a basis for both understanding human health and diagnosing, monitoring, and treating disease. The HCABrowser Biocondctor pacakge provides infrastructure for searching for, queerying, and accessing data help on the Human Cell Atlas's Data Coordination Platform (https://dss.data.humancellatlas.org/). Further changes to the package are planned to incorperate higer level functionality to upload user generated data to the the Human Cell Atlas platform.

This is a Biocondcutor package and can be installed using BiocManager.

## Install Bioconductor
if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("HCABrowser")

library(HCABrowser)

This package introduces the HCABrowser object used to connect to and perform opertions on the Human Cell Atlas

hca <- HCABrowser()
hca

The Human Cell Atlas Data Portal requires queries to be submitted against their schema. Given the schema is complicated and users may not want to learn it in order to search the Human Cell Atlas, we seek to offer an easier way for the user to explore the Human Cell Atlas.

First we want to see which fields and values of fields are available.

## Show fields and their respective abbreviations
hca %>% fields

## Show availiable values for a field (e.g. organ.text)
hca %>% values(organ.text)

## OR show all values for all fields
hca %>% values

The filter() and select() methods are used to query the Human Cell Atlas.

## Search for bundles regarding blood and that were no constructed with Smart-Seq2
hca <- hca %>% filter(organ.text == "blood" && library_construction_approach.text != "Smart-Seq2")
hca

## Include columns for 'project_title' and 'project_shortname'
hca <- hca %>% select(c('project_title', 'project_shortname'))
hca

Once the data bundles of interest are found, they can be downloaded and used to obtain data. We then use these bundles to download the expression matrices using the HCAMatrixBrowser package.

bundles <- hca %>% pullBundles

if (!requireNamespace("HCAMatrixBrowser"))
    BiocManager::install("HCAMatrixBrowser")

library(HCAMatrixBrowser)

loadHCAMatrix(bundles)

For my information, please refer to the package's vignette.

As with other Biocondcutor packages, the master branch indicates the development branch and the RELEASE_X_X branch indicates the current release branch.