nikolayoskolkov Goto Github PK

advancedpythoncourse

Material for advanced Python course 2019

amdirt

Check validity of AncientMetagenomeDir dataset

ameta

ancientmetagenomedir

Repository containing lists of all published ancient metagenome samples (and related)

clusteringhighdimensions

Here I demonstrate how to automatically detect the number of clusters in scRNAseq data

covid19

Corona infection related computations

deeplearningancientdna

Here I show how to use Convolutional Neural Networks (CNNs) for Ancient DNA analysis

deeplearningclinicaldiagnostics

Here I show how to utilize Bayesian Deep Learning using PyMC3 for making more accurate and safer predictions for biomedical applications

deeplearningdataintegration

Here I show how to use Deep Learning for biological and biomedical Data Integration.

deeplearningmicrobiome

deeplearningmicroscopyimaging

Here I demonstrate how to use Faster-RCNN and Mask-RCNN for cell detection using Human Protein Atlas (HPA) digital image data

deeplearningneanderthalintrogression

Here I deposite input files and Jupyter notebooks on detecting Neanderthal introgression analysis

deeplearningsinglecellbiology

Here I show how to use Deep Autoencoders for single cell RNA sequencing data analysis

dimreductsinglecell

Here I cover linear and non-linear dimension reduction techniques for single cell genomics

featureselectionintegromics

How to us univariate and multivariate feature selection for OMICs integration

genomicsnewclothes

Here I discuss common pitfalls in Genetics research due to the high-dimensional nature of genetic variation data that suffers from the Curse of Dimensionality

howlinearmixedmodelworks

howtobatchcorrectsinglecell

Here I explain batch-effects correction techniques for scRNAseq experiments

howtoinitializeumaptsne

Checking how tSNE and UMAP depend on different initialization scenarios

howumapworks

Here I explain the math behind UMAP and show how to program it from scratch in Python

iceman_fungi

Here we provide scripts used for analysis of fungal community in Iceman metagenomic data

integrativeomicsworkflow

Here we provide a primer-workflow for biological data integration analysis.

lmmfromscratch

Deriving and coding Linear Mixed Model (LMM) from scratch

lstmneanderthaldna

Implementation of LSTM for detecting regions of Neanderthal introgression in modern human genomes

normalizesinglecell

Comparison of single cell normalization strategies

oslobioinfoweek2022

plaguerandomsample

reml

Deriving and coding Linear Mixed Model in Restricted Maximum Likelihood (REML) approach

sbw2022

This is a teaching material for scRNAseq workshop within SBW2022

seurat

R toolkit for single cell genomics