scikit-posthocs: Pairwise multiple comparison tests in Python

Terpilowski, M. A.

doi:10.21105/joss.01169

Cited by 200 publications

(130 citation statements)

References 1 publication

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“…Any mRNA that rejected the null hypothesis (p < 0.05) was subjected to a post-hoc Dunn's Multiple Comparison Test with Benjamini-Krieger-Yekutieli two-stage false discovery rate correction [77]. These comparisons were completed using the SciPy [78] and scikit-posthocs [79] Python packages. Statistical significance between two values was determined using a two-tailed t test using Prism 7 (GraphPad, San Diego, CA, USA).…”

Section: Resultsmentioning

confidence: 99%

Modelling Lyssavirus Infections in Human Stem Cell-Derived Neural Cultures

Sundaramoorthy

Gödde

Farr

et al. 2020

Viruses

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Rabies is a zoonotic neurological infection caused by lyssavirus that continues to result in devastating loss of human life. Many aspects of rabies pathogenesis in human neurons are not well understood. Lack of appropriate ex-vivo models for studying rabies infection in human neurons has contributed to this knowledge gap. In this study, we utilize advances in stem cell technology to characterize rabies infection in human stem cell-derived neurons. We show key cellular features of rabies infection in our human neural cultures, including upregulation of inflammatory chemokines, lack of neuronal apoptosis, and axonal transmission of viruses in neuronal networks. In addition, we highlight specific differences in cellular pathogenesis between laboratory-adapted and field strain lyssavirus. This study therefore defines the first stem cell-derived ex-vivo model system to study rabies pathogenesis in human neurons. This new model system demonstrates the potential for enabling an increased understanding of molecular mechanisms in human rabies, which could lead to improved control methods.

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Section: Resultsmentioning

confidence: 99%

Modelling Lyssavirus Infections in Human Stem Cell-Derived Neural Cultures

Sundaramoorthy

Gödde

Farr

et al. 2020

Viruses

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“…A Kruskal-Wallis test was used to identify statistically significant differences across two or more groups, and a Mann-Whitney U test was used for pairwise tests using a Holm-Sidak correction for multiple hypothesis testing [71,72]. We used the scipy [73] stats implementation of the Kruskal-Wallis test and the scikit-learn post hoc processing [74] implementation of pairwise Mann-Whitney U tests. Spearman rank and Pearson correlation values were calculated using the scipy library [72].…”

Section: Resultsmentioning

confidence: 99%

Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures

et al. 2020

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Precision oncology has primarily relied on coding mutations as biomarkers of response to therapies. While transcriptome analysis can provide valuable information, incorporation into workflows has been difficult. For example, the relative rather than absolute gene expression level needs to be considered, requiring differential expression analysis across samples. However, expression programs related to the cell-of-origin and tumor microenvironment effects confound the search for cancer-specific expression changes. To address these challenges, we developed an unsupervised clustering approach for discovering differential pathway expression within cancer cohorts using gene expression measurements. The hydra approach uses a Dirichlet process mixture model to automatically detect multimodally distributed genes and expression signatures without the need for matched normal tissue. We demonstrate that the hydra approach is more sensitive than widely-used gene set enrichment approaches for detecting multimodal expression signatures. Application of the hydra analysis framework to small blue round cell tumors (including rhabdomyosarcoma, synovial sarcoma, neuroblastoma, Ewing sarcoma, and osteosarcoma) identified expression signatures associated with changes in the tumor microenvironment. The hydra approach also identified an association between ATRX deletions and elevated immune marker expression in high-risk neuroblastoma. Notably, hydra analysis of all small blue round cell tumors revealed similar subtypes, characterized by changes to infiltrating immune and stromal expression signatures.

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“…Analysis of cell numbers and EAG responses including statistical comparison and plotting was performed using Python (version 3.7.3, Python Software Foundation, www.python.org) based custom scripts. Those scripts utilize the SciPy ecosystems (www.scipy.org) modules SciPy (version 1.2.1) 112 , Numpy (version 1.16.2) 113 , Matplotlib (version 3.0.3) 114 , and Pandas (version 0.24.2) 115 , as well as the additional modules scikit-posthocs (version 0.5.1, https://github.com/maximtrp/scikit-posthocs) 116 , Seaborn (version 0.9.0) 117 , and localreg (version 0.2.1, https://github.com/sigvaldm/localreg).…”

Section: Methodsmentioning

confidence: 99%

Adult neurogenesis in the mushroom bodies of red flour beetles (Tribolium castaneum, Herbst) is influenced by the olfactory environment

Trebels

Dippel

Schaaf

et al. 2020

Sci Rep

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holometabolous insects, such as the noctuid moth Agrotis ipsilon 58 , as well as several beetle species 59 including the red flour beetle Tribolium castaneum 60. T. castaneum is a member of the largest insect order (Coleoptera) 61,62 and a major pest of stored cereal products 61,63,64. With its annotated genome sequence 26,65-67 , an expanding genetic toolbox 68-70 including strong systemic RNA interference (RNAi) 71-73 , and its relative longevity of up to two years 74 , T. castaneum represents an eligible beetle model for studying adult plasticity. We concentrated on olfaction which is supposed to be a main input into the mushroom bodies of T. castaneum 26 , to answer whether the adult persisting neurogenesis is genetically predetermined and continuation of developmental processes or if it is activity-dependent. Results Identification of newly born cells. To label adult-born cells, we used the 5-ethynyl-2′-desoxyuridine (EdU) method 75,76. With this method, we reliably and exclusively labelled the mushroom body neuroblasts and their progeny, while neurogenesis is not present in other areas of the cerebral ganglion of the red flour beetle (Fig. 1A). The neuroblasts were distinguished from their progeny based on their larger size (Fig. 1B). We confirmed that in T. castaneum, adult-born Kenyon cells usually derive from two neuroblasts (NB) per hemisphere and send their axons into the core of the mushroom body peduncle (PED) and lobes as shown by Zhao and colleagues 60 (Fig. 1C). The neuronal identity of the EdU labelled cells was verified by demonstrating co-localization with the reporter signal (Fig. 1D-D") in the neuron labelling EF1-B-DsRed line 77 , as well as immunohistochemical staining against the glia cell marker reversed polarity 78 resulting in no co-localization (Fig. 1E-E").

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scikit-posthocs: Pairwise multiple comparison tests in Python

Cited by 200 publications

References 1 publication

Modelling Lyssavirus Infections in Human Stem Cell-Derived Neural Cultures

Modelling Lyssavirus Infections in Human Stem Cell-Derived Neural Cultures

Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures

Adult neurogenesis in the mushroom bodies of red flour beetles (Tribolium castaneum, Herbst) is influenced by the olfactory environment

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