Repositories list

• CAMISIM_reproducibility

  Public
  To reproduce some results from "CAMISIM: simulating metagenomes and microbial communities". Authors: Simon Konnov, Ciara Makievskaya, Ruslan Gumerov

  reproducibilitymetagenomescamisim

  Jupyter Notebook

  •1•1•0•0•Updated May 24, 2019May 24, 2019

• Host-Taxon-Predictor

  Public
  A Tool for Predicting Taxon of the Host of a Newly Discovered Virus

  Python

  •0•0•0•0•Updated May 21, 2019May 21, 2019

• GOATOOLS_repr

  Public
  Воспроизведение некоторых результатов из статьи про GOATOOLS: A Python library for Gene Ontology analyses (DOI:10.1038/s41598-018-28948-z)

  Python

  •0•0•0•0•Updated May 21, 2019May 21, 2019

• ScScope

  Public
  Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning

  Jupyter Notebook

  •0•0•0•0•Updated May 21, 2019May 21, 2019

• Evolutionarily-informed-deep-learning

  Public
  Авторы: Бердникович Е, Раздобарин З., Третьяков Д.

  Jupyter Notebook

  •0•0•0•0•Updated May 21, 2019May 21, 2019

• codon_bias

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 21, 2019May 21, 2019

• Ab-Initio-Protein-Structure-Prediction

  Public
  Using materials and methods of the article "Ab initio protein structure prediction of CASP III targets using ROSETTA" written by Kim T. Simons, Rich Bonneau, Ingo Ruczinski and David Baker, we conducted ab initio folding to generate structures consistent with both the local and nonlocal interactions responsible for protein stability. To generate…

  HTML

  •0•4•0•0•Updated May 20, 2019May 20, 2019

• Convolutional-neural-networks_ncRNA

  Public
  To reproduce some results from "Convolutional neural networks for classification of alignments of non-coding RNA sequences"

  Jupyter Notebook

  •

  MIT License

  •0•0•1•0•Updated May 20, 2019May 20, 2019

• treeWAS

  Public
  Test of treeWAS tool described in the paper "A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination" (Caitlin Collins, Xavier Didelot, 2018, PLOS Computational Biology).

  Jupyter Notebook

  •0•0•0•0•Updated May 20, 2019May 20, 2019

• Phenograph

  Public
  Single cell RNA-seq and clusterization (phenograph)

  Python

  •0•1•0•0•Updated May 20, 2019May 20, 2019

• QIIME2-mock-community-evaluations

  Public
  Korkunova, Nesterenko, Raldugina. Taxonomic classification of marker-gene sequences is an important step in microbiome analysis.

  0•0•0•0•Updated May 20, 2019May 20, 2019

• Splicing-factor-1-modulates-dietary-restriction-and-TORC1-pathway-longevity-in-_C.-elegans_

  Public
  Re-analysis of the publication

  Python

  •0•0•0•0•Updated May 20, 2019May 20, 2019

• CichlidsGeneFlow

  Public
  Воспроизведение Fig 3. из статьи Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

  Jupyter Notebook

  •0•0•0•0•Updated May 20, 2019May 20, 2019

• FreePSI

  Public
  Трифонова, Волобуева

  Jupyter Notebook

  •0•0•0•0•Updated May 20, 2019May 20, 2019

• Application-of-Uncertainpy-for-Izhikevich-Neuron-Model-Quantification

  Public
  Authors: Anton Izzi, Stanislav Tikhonov, Anton Vlasov. In this project we used Uncertainpy module for Python to quantify Izhikevich neuron models with different parameters to evaluate the module's quality.

  Jupyter Notebook

  •0•0•0•0•Updated May 20, 2019May 20, 2019

• Giggle

  Public
  Reproducibility of visualization of GIGGLE scores from the relationships between 15 genomic states across different cell types and tissues predicted by ChromHMM for Roadmap and MyoD ChIP-seq peaks

  Jupyter Notebook

  •1•0•0•0•Updated May 20, 2019May 20, 2019

• Genome-Expansion

  Public
  To reproduce some plots from the article "Evolutionary Rewiring of Human Regulatory Networks by Waves of Genome Expansion" (Marnetto et al, Am J Hum Genet, 2018)

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 15, 2018May 15, 2018

• RNA-DNA

  Public
  Reproducibility of some plots from GRID-Seq paper (Xiao Li et al., 2018 Nature Biotechnology) for the purpose of learning Python for computational biology.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated May 15, 2018May 15, 2018

• CRISPR-Cas3

  Public
  Reproducibility of some plots from "Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation" paper (Künne et al., 2016 Molecular Cell) for the purpose of learning Python for computational biology.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 15, 2018May 15, 2018

• TADs

  Public
  Reproducibility of some plots from "Comparison of computational methods for Hi-C data analysis" paper (Forcato et al., 2017 Nature Methods) for the purpose of learning Python for computational biology.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated May 15, 2018May 15, 2018

• uORF

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 15, 2018May 15, 2018

• Cell-Cycle-at-Single-Cell-Resolution

  Public
  To reproduce some results from "Cell-cycle dynamics of chromosomal organization at single-cell resolution" (Nagano et al, Nature, 2017)

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 14, 2018May 14, 2018

• Single-cell-Alzheimer

  Public
  To reproduce some results from "A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease" (H. Keren-Shaul et al, Cell, 2017)

  Jupyter Notebook

  •0•0•0•0•Updated May 14, 2018May 14, 2018

• Ribo-seq

  Public
  Reproducibility of some plots from "Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling" paper (Mohammad et al., 2016 Cell Reports) for the purpose of learning Python for computational biology.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated May 14, 2018May 14, 2018

• instructions

  Public
  This repo contains instructions for the students about git usage and projects update.

  0•0•0•0•Updated May 11, 2018May 11, 2018