maxxim333

Analysis_of_Yeast_mRNA

This was an exercise to retreive information from mRNA data of yeast genome annotation using Bash and construct a couple of graphs using R

API_UniProt

In this work I use API to retrieve information of a customized list of proteins from the famous protein database UniProt.

drug-induced_morphology_changes_quantification

I treated iPSC with FDA approved drugs, stained them with neurite and nuclear markers and obtained confocal fluorescent images. Now, the goal is to quantify the change of neurites in each condition, namely 3 parameters: amount of trunk-branches (neurite branching from the body of the cell), non-trunk branching and mean length of neurites.

Genomic_Data_Analysis

My biggest bioinformatic venture yet. This is an integrated bottom-up analysis of Genomic data, simulating a real bioinformatic pipeline starting from raw transcriptome sequencing data. Three programming languages are used: shell, python2.7 and R 3.5.1.

Methylome_Data_Wrangling

Exercise on Data Wrangling using dplyr and tibble libraries of R

Neural_Networks

This work performs two different types of Neural Networks training and 5-fold CV, each one on three datasets that differ in three of the attributes. It uses 100 iterations with random seeds and after all iterations are completed, it calculates the average of different performance metrics

PCA_SVM

PCA and faces recognition using SVM

random_forest_hyperparameters_tunning

In this work I use Random Forest tool on two datasets and find the optimal hyperparameters for the algorithm on both datasets and compare their performance.

RNAseq_analysis

Exercise of RNAseq alignment against reference, creation of bam, bigwig, RPKM calculation and samples comparison

upm

maxxim333/Genomic_Data_Analysis

My biggest bioinformatic venture yet. This is an integrated bottom-up analysis of Genomic data, simulating a real bioinformatic pipeline starting from raw transcriptome sequencing data. Three programming languages are used: shell, python2.7 and R 3.5.1.

maxxim333/drug-induced_morphology_changes_quantification

I treated iPSC with FDA approved drugs, stained them with neurite and nuclear markers and obtained confocal fluorescent images. Now, the goal is to quantify the change of neurites in each condition, namely 3 parameters: amount of trunk-branches (neurite branching from the body of the cell), non-trunk branching and mean length of neurites.

maxxim333/upm

maxxim333/Analysis_of_Yeast_mRNA

This was an exercise to retreive information from mRNA data of yeast genome annotation using Bash and construct a couple of graphs using R

maxxim333/API_UniProt

In this work I use API to retrieve information of a customized list of proteins from the famous protein database UniProt.

maxxim333/Methylome_Data_Wrangling

Exercise on Data Wrangling using dplyr and tibble libraries of R

maxxim333/Neural_Networks

This work performs two different types of Neural Networks training and 5-fold CV, each one on three datasets that differ in three of the attributes. It uses 100 iterations with random seeds and after all iterations are completed, it calculates the average of different performance metrics

maxxim333/PCA_SVM

PCA and faces recognition using SVM

maxxim333/random_forest_hyperparameters_tunning

In this work I use Random Forest tool on two datasets and find the optimal hyperparameters for the algorithm on both datasets and compare their performance.

maxxim333/RNAseq_analysis

Exercise of RNAseq alignment against reference, creation of bam, bigwig, RPKM calculation and samples comparison

maxxim333/Assignment3_ruby

maxxim333/Assignment4

maxxim333/assignment5_QueriesSPARQL

maxxim333/Biomarkers

Using R, biomarkers were defined selecting the most relevant genes after a PCA on a data from a table of gene expression VS cell-type.

maxxim333/Collinear_Points

Here I am learning python and pyspark in an exercise where I have to create a script that from an input consisting in set of points, returns groups of collinear points.

maxxim333/Files_reprocessing_and_Multiple_Sequence_Alignment

Here I perform a iterative MSA (with MUSCLE) on FASTA sequences of many files. The shell script does a bioinformatic reprocessing so the input is correct.

maxxim333/fluorescence_tracking

Plotting and Fourier transformation of cell fluorescence tracking VS time

maxxim333/Neural_Networks_2

This is a work similar to the in maxxim333/Neural_Networks repository. This time, after cross-validation and creation of .rbf files, "sensitivity" parameter is calculated INDIVIDUALLY for each gene from a custom list of genes. This is done for both datasets and then a scatter plot is made to compare performance of each gene in each of the datasets.

maxxim333/orthologs_vs_evolutionary_distance

The goal of this work is to find what relationship does the evolutionary distance of a specie from Homo Sapiens have on the number of orthologs that appear for that specie for any of the 6000 clinically relevant human genes. In this exercise, I work with .nwk files to retreive evolutionary distances between a set of proteins of different species using PhyloTree module of Python, launch a shell script to get the orthologues of a subset oh about 6000 human genes, create a file where for each specie, a number of times the protein belonging to that specie appears in the ortholog list in Homo Sapiens and finally launch and R script that creates a plot and linear regression showing the negative correlation between evolutionary distance and number of orthologs.

maxxim333/pandas

This is an exercise I made as a preparation for an interview for a position in a financial data. The company's main specific requirement was knowledge of pandas module, so I made as much things in pandas a possible.

maxxim333/Python_Health_Data

Training Python applied to Biostatistics

maxxim333/rcommander

Performing Factor Analysis and Correspondence Analysis using R Commander and FactorMineR package

maxxim333/Ruby_Assignment1

Simulating planting seed and updating databases

maxxim333/ruby_assignment2

Intensive integration using Web APIs - Construction of protein interaction network

maxxim333/scooter_data_analysis

This is an exercise I helped a friend to do for his interview. Since all this code is mine, I feel I'm entitled to post it here. It was for a data analyst job in a scooter-renting company. The input file they provided was a csv with logs of users and timestamps of their activities. The goal was to create "Sessions" of each users in which each session is defined by certain characteristics. Then I needed to find out the "peak of demand" for scooters defined by the time period where there is the biggest overlap of sessions. The images I provide are divided in two and there are two .py files. One takes as an input the csv table provided by the interviewers and generates a file with session ids and the other takes this file as input and outputs a sorted array of timestamps and their corresponding amount of overlapping sessions. The first element is the answer to the problem: the time of the year with the most demand of scooters.

maxxim333/Spatial-Statistics

Analyzing a cross-section of a stomach mucous membrane (a dataset with spatial characteristics) using base R and spatstat package

maxxim333/Transcriptome-Analysis-and-PCA

Using R, transcriptome of WT and mutant (with and without compensation) cells are analysed and PCA is performed to find genes affecting the global transcriptome the most.

maxxim333/visited_places

I wanted a resource where I can annotate places I visited/lived in the world but every site either uses it spy on you or eventually asks for money, so I programmed one in R. It takes as an argument a file with coordinates and creates a map with points.

maxxim333/work