Daniel Schlauch
5 Papers
Daniel Schlauch is an academic researcher. The author has contributed to research in topics: Computer science & Biology. The author has an hindex of 2, co-authored 3 publications.
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Papers
RNA-Seq analysis in MeV
Eleanor Howe,Raktim Sinha,Daniel Schlauch,John Quackenbush +3 more
- 05 Oct 2011
TL;DR: A significant enhancement to MeV is reported that allows analysis of RNA-Seq data with these familiar, powerful tools, addressing the differences in analysis requirements between this data type and traditional gene expression data.
366
Higher-order correction of persistent batch effects in correlation networks
Soel Micheletti,Daniel Schlauch,John Quackenbush,Marouen Ben Guebila +3 more
TL;DR: COBRA is a method for computing a batch-corrected gene co-expression matrix based on estimating a conditional covariance matrix, which estimates a reduced set of parameters expressing the co-expression matrix as a function of the sample covariates, allowing control for continuous and categorical covariates.
The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks
Marouen Ben Guebila,Tian Wang,Camila M. Lopes-Ramos,Viola Fanfani,Des Weighill,Rebekka Burkholz,Daniel Schlauch,Joseph N. Paulson,Michael Altenbuchinger,K. Shutta,Abhijeet R. Sonawane,James T. Lim,Genís Calderer,David G.P. van IJzendoorn,Daniel Morgan,Alessandro Marin,Cho Yi Chen,Qi Song,Enakshi Saha,Dawn L. DeMeo,Megha Padi,John Platig,Marieke L. Kuijjer,Kimberly Glass,John Quackenbush +24 more
TL;DR: The Network Zoo as mentioned in this paper is a collection of open-source methods to infer gene regulatory networks, conduct differential network analyses, estimate community structure, and explore the transitions between biological states, and demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia.
The Network Zoo: a multilingual package for the inference and analysis of biological networks
Marouen Ben Guebila,Tian Wang,Camila M. Lopes-Ramos,Viola Fanfani,Deborah Weighill,Rebekka Burkholz,Daniel Schlauch,Joseph N. Paulson,Michael Altenbuchinger,Abhijeet Sonanwane,James T. Lim,Genís Calderer,David G.P. van IJzendoorn,Daniel Morgan,Alessandro Marin,Cho Yi Chen,A. Song,K. Shutta,Dawn L. DeMeo,Megha Padi,John Platig,Marieke L. Kuijjer,Kimberly Glass,John Quackenbush +23 more
TL;DR: The netZoo toolkit analyzed the multi-omic data from the Cancer Cell Line Encyclopedia by inferring gene regulatory networks for each cancer cell line and associating network features with other phenotypic attributes such as drug sensitivity to identify transcription factors that play a critical role in both drug resistance and cancer development in melanoma.
An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks
Marouen Ben Guebila,Deborah Weighill,Camila M. Lopes-Ramos,Rebekka Burkholz,Romana T. Pop,Kalyan Palepu,Mia Shapoval,Maud Fagny,Daniel Schlauch,Kimberly Glass,Michael Altenbuchinger,Marieke L. Kuijjer,John Platig,John Quackenbush +13 more
TL;DR: Jupyter notebooks allow developers to combine text, code and code output elements in an integrated executable document so that complex analyses can be reproduced, thus also allowing production of tutorials and educational vignettes.