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added zenodo DOIs
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tsoelter committed Nov 28, 2023
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241 changes: 241 additions & 0 deletions .zenodo.json
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{
"metadata": {
"contributors": [
{
"affiliations": [
{
"id": "008s83205",
"name": "University of Alabama at Birmingham"
}
],
"person_or_org": {
"family_name": "Lasseigne",
"given_name": "Brittany N.",
"identifiers": [
{
"identifier": "0000-0002-1642-8904",
"scheme": "orcid"
}
],
"name": "Lasseigne, Brittany N.",
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},
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"title": {
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}
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"name": "University of Alabama at Birmingham"
}
],
"person_or_org": {
"family_name": "Soelter",
"given_name": "Tabea M.",
"identifiers": [
{
"identifier": "0000-0003-1654-4240",
"scheme": "orcid"
}
],
"name": "Soelter, Tabea M.",
"type": "personal"
},
"role": {
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"title": {
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{
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"name": "University of Alabama at Birmingham"
}
],
"person_or_org": {
"family_name": "Howton",
"given_name": "Timothy C.",
"identifiers": [
{
"identifier": "0000-0002-9423-0135",
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}
],
"name": "Howton, Timothy C.",
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},
"role": {
"id": "researcher",
"title": {
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"given_name": "Amanda D.",
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"identifier": "0000-0002-1186-3114",
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],
"name": "Clark, Amanda D.",
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"person_or_org": {
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"given_name": "Vishal H.",
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"identifier": "0000-0001-6990-0267",
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],
"description": "<p>Initial release:</p>\n<p>The code and results accompany the &quot;Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq&quot; manuscript.</p>",
"identifiers": [
{
"identifier": "10.5281/zenodo.10211623",
"scheme": "doi"
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],
"publication_date": "2023-11-27",
"publisher": "Zenodo",
"related_identifiers": [
{
"identifier": "https://github.com/lasseignelab/230313_TS_CCCinHumanAD/tree/v1.0.0",
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"rights": [
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"description": {
"en": "A short and simple permissive license with conditions only requiring preservation of copyright and license notices. Licensed works, modifications, and larger works may be distributed under different terms and without source code."
},
"id": "mit",
"props": {
"scheme": "spdx",
"url": "https://opensource.org/licenses/MIT"
},
"title": {
"en": "MIT License"
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}
],
"title": "lasseignelab/230313_TS_CCCinHumanAD: Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq"
}
}

7 changes: 6 additions & 1 deletion README.Rmd
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Expand Up @@ -52,14 +52,19 @@ Manuscript figures:
fs::dir_tree("src/manuscript_figures/")
```

## Code and Data Availability
Data: [![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.10214497-blue)](https://doi.org/10.5281/zenodo.10214497)
Docker Images: [![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.10214660-blue)](https://doi.org/10.5281/zenodo.10214660)
GitHub Repository: [![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.10211622-blue)](https://doi.org/10.5281/zenodo.10211622)

## Docker
We performed all analyses in docker with R version 4.1.3. The repository with all the Docker images used for this project can be found on Docker Hub at [tsoelter/rstudio_ccc_ad](https://hub.docker.com/repository/docker/tsoelter/rstudio_ccc_ad/general). While individual docker image tags are noted in every script, we provide an overview of analyses and their associated tags below:

Tag | Associated Analyses
--- | ---
1.0.1 | Pre-processing of Morabito et al., 2021
1.0.3 | Pre-processing of Lau et al., 2020, CCC, and JI
1.0.5 | GRNs, pseudo-bulking, DEA, and biological activity
1.0.5 | GRNs, pseudo-bulking, DEA, biological activity, and plotting

## Lasseigne Lab

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21 changes: 15 additions & 6 deletions README.md
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@@ -1,6 +1,6 @@
README
================
2023-11-27
2023-11-28

# Altered Glia-Neuron Communication in Alzheimer’s Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq

Expand Down Expand Up @@ -109,6 +109,15 @@ Manuscript figures:
## +-- figure_S3.Rmd
## \-- figure_S4.Rmd

## Code and Data Availability

Data:
[![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.10214497-blue)](https://doi.org/10.5281/zenodo.10214497)
Docker Images:
[![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.10214660-blue)](https://doi.org/10.5281/zenodo.10214660)
GitHub Repository:
[![DOI](https://img.shields.io/badge/DOI-10.5281/zenodo.10211622-blue)](https://doi.org/10.5281/zenodo.10211622)

## Docker

We performed all analyses in docker with R version 4.1.3. The repository
Expand All @@ -118,11 +127,11 @@ Hub at
While individual docker image tags are noted in every script, we provide
an overview of analyses and their associated tags below:

| Tag | Associated Analyses |
|-------|----------------------------------------------------|
| 1.0.1 | Pre-processing of Morabito et al., 2021 |
| 1.0.3 | Pre-processing of Lau et al., 2020, CCC, and JI |
| 1.0.5 | GRNs, pseudo-bulking, DEA, and biological activity |
| Tag | Associated Analyses |
|-------|--------------------------------------------------------------|
| 1.0.1 | Pre-processing of Morabito et al., 2021 |
| 1.0.3 | Pre-processing of Lau et al., 2020, CCC, and JI |
| 1.0.5 | GRNs, pseudo-bulking, DEA, biological activity, and plotting |

## Lasseigne Lab

Expand Down

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