https://github.com/bioconductor/hcabrowser

Browse the Human Cell Atlas data portal
https://github.com/bioconductor/hcabrowser

bioconductor human-cell-atlas

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Browse the Human Cell Atlas data portal

• Host: GitHub
• URL: https://github.com/bioconductor/hcabrowser
• Owner: Bioconductor
• Created: 2018-05-16T18:15:14.000Z (over 6 years ago)
• Default Branch: devel
• Last Pushed: 2023-03-10T18:15:34.000Z (almost 2 years ago)
• Last Synced: 2024-05-09T07:47:28.503Z (8 months ago)
• Topics: bioconductor, human-cell-atlas
• Language: R
• Homepage:
• Size: 516 KB
• Stars: 8
• Watchers: 11
• Forks: 4
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        

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.

- API: https://dss.data.humancellatlas.org/

- schema https://github.com/HumanCellAtlas/metadata-schema

- typical tasks: https://github.com/HumanCellAtlas/data-consumer-vignettes