PACHTERLAB.GITHUB.IO

UC Berkeley Mathematical and Computational Biology » Software

Molecular and Cell Biology. And Electrical Engineering and Computer Science. Software developed in the Pachter group and still under active development in the group. 2015) RNA-Seq differential analysis. 2015) Quantitative modeling of transcriptome-wide RNA structure-probing experiments. 2013) Computing genome assembly likelihoods. Software developed in the Pachter group but now maintained/developed elsewhere. 2016) Scaffolding with assembly likelihood optimization (now supported by Atif Rahman). These pr...

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Molecular and Cell Biology. And Electrical Engineering and Computer Science. Software developed in the Pachter group and still under active development in the group. 2015) RNA-Seq differential analysis. 2015) Quantitative modeling of transcriptome-wide RNA structure-probing experiments. 2013) Computing genome assembly likelihoods. Software developed in the Pachter group but now maintained/developed elsewhere. 2016) Scaffolding with assembly likelihood optimization (now supported by Atif Rahman). These pr...

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UC Berkeley Mathematical and Computational Biology » Software | pachterlab.github.io Reviews

https://pachterlab.github.io

Molecular and Cell Biology. And Electrical Engineering and Computer Science. Software developed in the Pachter group and still under active development in the group. 2015) RNA-Seq differential analysis. 2015) Quantitative modeling of transcriptome-wide RNA structure-probing experiments. 2013) Computing genome assembly likelihoods. Software developed in the Pachter group but now maintained/developed elsewhere. 2016) Scaffolding with assembly likelihood optimization (now supported by Atif Rahman). These pr...

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pachterlab.github.io

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PROBer: A general toolkit for analyzing sequencing-based 'toeprinting' assays

http://pachterlab.github.io/PROBer

July 15, 2015 PROBer website launched. June 26, 2016 PROBer v0.2.0 was uploaded. Created by Bo Li. The header background is adopted from Vossman.

2

Pachter Lab homepage

http://pachterlab.github.io/index.html

The Pachter Lab develops computational and experimental methods for genomics. We are currently focused on the development of single cell sequencing based technologies and their application to RNA biology. The computational challenges we are addressing involve the analysis of high-dimensional data. Theorems are sometimes proven, experiments are occasionally successful, and usable software is distributed on GitHub.

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psturmfels.github.io

Sleuth

http://psturmfels.github.io/2016/Sleuth

Studying computer science at University of Michigan; interests include theory of algorithms, natural language processing, and iOS development. Tool that performs differential expression analysis on quantified reads from kallisto. Sleuth is novel both in its use of statistical bootstraps to understand differential gene expression, and in its use of Shiny. To provide in-browser, interactive analyses of RNA-seq experiments. If you are interested in using sleuth, see the sleuth homepage.

psturmfels.github.io

The Lair

http://psturmfels.github.io/2016/the_lair

Studying computer science at University of Michigan; interests include theory of algorithms, natural language processing, and iOS development. Is a system and website that the Pachter Lab. And I made to address this problem: It hosts interactive re-analyses of publicly available RNA-seq data. The development of this system work was published in an article in BMC Bioinformatics. The reason the Lair is so powerful is that the re-analyses of papers are performed automatically by a back-end Snakemake.

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pachterlab.github.io

UC Berkeley Mathematical and Computational Biology » Software

Molecular and Cell Biology. And Electrical Engineering and Computer Science. Software developed in the Pachter group and still under active development in the group. 2015) RNA-Seq differential analysis. 2015) Quantitative modeling of transcriptome-wide RNA structure-probing experiments. 2013) Computing genome assembly likelihoods. Software developed in the Pachter group but now maintained/developed elsewhere. 2016) Scaffolding with assembly likelihood optimization (now supported by Atif Rahman). These pr...

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