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1_proteomics_data_analysis

This repo will contain scripts, functions and snippets of code useful for processing and analyzing different types of proteomics data

bioconda-recipes

Conda recipes for the bioconda channel.

cleaning-data-project

cleaning_data_final_project

course-exploratory-data-analysis

This repo is to share all the code I will use during the Course course, Exploratory Data Analysis with R

courses

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

datasharing

The Leek group guide to data sharing

delete_mq_junk

This repo would contain the script for deleting junk after MaxQuant search

differential_expression_analysis_msstats

Short script summarizing the workflow for pre-processing and differential analysis of LFQ MaxQuant data in MSsstats

dotfiles

some of my dotfiles

drawproteins

Creating package to draw proteins from Uniprot API

enrichroast

Repo containing scripts and functionts to run limma::roast enrichment analyses

fasta_processing

final_project_ml_course

Course-John Hopkins Practical Machine Learning Course. Final Project

first_project_eda_coursera

First project for the course of exploratory data analysis

fragenterminomics

Pipeline for extracting and exploring nterminomics data from FragPipe and TMT-Integrator

fragterminomics

Annotation and processing of peptides from FragPipe search results

gbm_manuscript_data_analysis

Data processing and analysis of database search and quant proteomics results from GBM patients - Initial vs Recurrent conditions

getting_cleaning_data_quizweek2

Workspace for quiz 2 of the Coursera Course

gsea_roast

Scripts and functions to run Limma-roast

hello-world

Just to share random stuff about what I'll do with my GitHub account

hpar

A simple interface to the Human Protein Atlas

limma_fdr_on_feature_subset

This repo will contain scripts to execute limma and then apply multiple testing correction on a subset of features (i.e. semi-tryptic peptides; ecoli proteins, etc)

limma_multi_group

Script for executing a general F-test on a protein/gene expression dataset with > 2 groups

limma_two_groups

This repo contains a small script for generating a report after simple paired DE with limma

limma_w_patient-matched_design

This repo will contain a guideline document for the execution of a differential expression analysis with limma including a patient random effect in the model

mapping_peptides_to_proteins_from_fasta_file

This repo contains a script for mapping peptide sequences arousing from database search algorithms to their corresponding proteins in a fasta file

markdown-practice

This is a repo to practice Markdown

minimal_fragterminomics

simplified version of fragterminomics

mq_msms_2_percolator_tab

This repo would contain a script for transforming the `msms.txt` output from MaxQuant into a `.tab` file that can be used as an input for Percolator