IHC analysis of placental tissue in COVID-19

<- dataset repository

Inflammatory Responses in the Placenta upon SARS-CoV-2 Infection Late in Pregnancy - analysis of IHC data Lissenya B. Argueta*, Lauretta A. Lacko*, Yaron Bram*, Takuya Tada, Lucia Carrau, André Figueiredo Rendeiro, Tuo Zhang, Skyler Uhl, Brienne C. Lubor, Vasuretha Chandar, Cristianel Gil, Wei Zhang, Brittany Dodson, Jeroen Bastiaans, Malavika Prabhu, Sean Houghton, David Redmond, Christine M. Salvatore, Yawei J. Yang, Olivier Elemento, Rebecca N. Baergen, Benjamin R. tenOever, Nathaniel R. Landau, Shuibing Chen, Robert E. Schwartz, Heidi Stuhlmann. iScience 2022. doi:10.1016/j.isci.2022.104223

Organization

• The metadata directory contains metadata relevant the samples and acquired data
• The src directory contains source code used to analyze the data
• Raw data should be under the data directory after download from Zenodo.
• Outputs from the analysis will be present in a results directory.

Reproducibility

Running

To see all available steps type:

$ make

To reproduce analysis using the pre-preocessed data, one would so:

$ make help
$ make requirements   # install python requirements using pip
$ make download_data  # download processed from Zenodo
$ make analysis       # run the analysis scripts

Requirements

• Python 3.7+ (was run on 3.9.2)
• Python packages as specified in the requirements file - install with make requirements or pip install -r requirements.txt. It is paramount to have scikit-image>=0.18.2!