jwiarda
Swine Immunologist - National Animal Disease Center, USDA; research emphases = porcine/mucosal/viral immunology
Ames, Iowa, USA
Pinned Repositories
scRNAseq_PBMCs
Scripts & figures used to finish scRNA-seq analysis from seven porcine PBMC samples, detailed in the manuscript "Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing" by Herrera-Uribe & Wiarda et al, 2021 (Preprint), available at https://doi.org/10.1101/2021.04.02.438107.
Intraepithelial_T_cells
Code associated with PERMANOVA and NMDS analyses of intraepithelial T cell data prepared for manuscript published in Frontiers in Immunology: "Intraepithelial T cells diverge by intestinal location as pigs age" by Wiarda et. al. 2020.
PorcinePBMCs_bulkRNAseq_scRNAseq
Scripts used for analysis of bulk RNA-seq, NanoString, and single-cell RNA-seq data from porcine PBMCs in the manuscript "Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing" by Herrera-Uribe & Wiarda et al, 2021 (Preprint), available at https://doi.org/10.1101/2021.04.02.438107.
Basic_Rstats
Code for some basic statistical tests in R; set up for beginner R users from the lab to use as practice/template.
scRNAseqEpSI_Pilot
Pilot study - single-cell RNA sequencing analysis of epithelial cells from pig small intestinal tract
scRNAseq_Porcine_Ileum_PBMC
TB_SkinTest_RNAseq
R code, inputs, and outputs associated with analysis of 82-Cattle skin testing data for Carly.
EarlyTB_RNAseq
RNAseq DGE analysis of whole blood from TB infected and uninfected cattle at early post-infection time points. A = moderately infected cattle; B = severely infected cattle; C = uninfected cattle. XvsY indicates upregulated genes more abundant in X, while downregulated genes more abundant in Y.
FlowCytometry_HighDimAnalysis_TIELs_WeaningAge
FS27_PBMC_scRNAseq
jwiarda's Repositories
jwiarda/scRNAseq_ChronicMastitis_MilkBlood
jwiarda/FS27_PBMC_scRNAseq
jwiarda/FlowCytometry_HighDimAnalysis_TIELs_WeaningAge
jwiarda/scRNAseq-STomics_PeyersPatches_IleumVsJejunum
jwiarda/FS27_WholeBlood_BulkRNAseq
jwiarda/NG10_DissertationScripts
Scripts for analysis of T-IELs and microbiota data in dissertation chapter 5.
jwiarda/scRNAseqEpSI_Pilot
Pilot study - single-cell RNA sequencing analysis of epithelial cells from pig small intestinal tract
jwiarda/scRNAseq_Porcine_Ileum_PBMC
jwiarda/Basic_Rstats
Code for some basic statistical tests in R; set up for beginner R users from the lab to use as practice/template.
jwiarda/scRNAseq_PBMCs
Scripts & figures used to finish scRNA-seq analysis from seven porcine PBMC samples, detailed in the manuscript "Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing" by Herrera-Uribe & Wiarda et al, 2021 (Preprint), available at https://doi.org/10.1101/2021.04.02.438107.
jwiarda/Intraepithelial_T_cells
Code associated with PERMANOVA and NMDS analyses of intraepithelial T cell data prepared for manuscript published in Frontiers in Immunology: "Intraepithelial T cells diverge by intestinal location as pigs age" by Wiarda et. al. 2020.
jwiarda/TB_SkinTest_RNAseq
R code, inputs, and outputs associated with analysis of 82-Cattle skin testing data for Carly.
jwiarda/EarlyTB_RNAseq
RNAseq DGE analysis of whole blood from TB infected and uninfected cattle at early post-infection time points. A = moderately infected cattle; B = severely infected cattle; C = uninfected cattle. XvsY indicates upregulated genes more abundant in X, while downregulated genes more abundant in Y.