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@Reproducibility-FBB-MSU

Reproducibility-FBB-MSU

We promote learning of python programming for computational biology through reproducibility of recent papers.

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  1. Ab-Initio-Protein-Structure-Prediction 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 cond…

    HTML 4

  2. Phenograph Phenograph Public

    Single cell RNA-seq and clusterization (phenograph)

    Python 1

  3. CAMISIM_reproducibility CAMISIM_reproducibility Public

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

    Jupyter Notebook 1 1

  4. RNA-DNA 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 2

  5. TADs 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 biol…

    Jupyter Notebook 1

  6. instructions instructions Public

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

Repositories

Showing 10 of 25 repositories
  • CAMISIM_reproducibility Public

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

    Reproducibility-FBB-MSU/CAMISIM_reproducibility’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated May 24, 2019
  • Host-Taxon-Predictor Public

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

    Reproducibility-FBB-MSU/Host-Taxon-Predictor’s past year of commit activity
    Python 0 0 0 0 Updated May 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)

    Reproducibility-FBB-MSU/GOATOOLS_repr’s past year of commit activity
    Python 0 0 0 0 Updated May 21, 2019
  • ScScope Public

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

    Reproducibility-FBB-MSU/ScScope’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated May 21, 2019
  • Evolutionarily-informed-deep-learning Public

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

    Reproducibility-FBB-MSU/Evolutionarily-informed-deep-learning’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated May 21, 2019
  • codon_bias Public
    Reproducibility-FBB-MSU/codon_bias’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated May 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…

    Reproducibility-FBB-MSU/Ab-Initio-Protein-Structure-Prediction’s past year of commit activity
    HTML 4 0 0 0 Updated May 20, 2019
  • Convolutional-neural-networks_ncRNA Public

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

    Reproducibility-FBB-MSU/Convolutional-neural-networks_ncRNA’s past year of commit activity
    Jupyter Notebook 0 MIT 0 1 0 Updated May 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).

    Reproducibility-FBB-MSU/treeWAS’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated May 20, 2019
  • Phenograph Public

    Single cell RNA-seq and clusterization (phenograph)

    Reproducibility-FBB-MSU/Phenograph’s past year of commit activity
    Python 1 0 0 0 Updated May 20, 2019
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