mcjmigdal
Bioinformatician. Expertising in NGS data analysis. Passionate about biology, ML and programming.
IIMCBPoland
Pinned Repositories
xcore
midasHLA
R package enabling statistical association analysis and using immunogenetic data transformation functions for HLA amino acid fine mapping, analysis of HLA evolutionary divergence as well as HLA-KIR interactions.
.doom.d
macs2_replicates
Calling peaks with macs2 and combining infromation from replicates using Fisher method
RNA-seq_data_analysis_course_for_biologists_may_2018
The goal of the course is to introduce basic RNA-seq data analysis, starting from experiment design and raw files to functional data analysis that can be performed using PC only. In brief, the content of the course will cover: general knowledge on RNA-seq library preparation (which kit/technology should I use and why? how many replicates? how deep should I sequence my samples?), quality check and filtering of the reads (including adapter trimming, rRNA removal), read alignment/quasi-mapping (can I perform read mapping on my PC without losing its specificity and efficacy?), performing gene counts (assigning reads to provided gene annotation), data normalization (which normalization types should I apply to my data?), differential expression data analysis, basic data visualization, functional analysis (GO terms, pathway analysis).
scripts
Usefull scripts
shiitake
shiitake mini-project
sumsamstats
summarising outputs of samtools stats with ATAC-seq qc in mind
mcjmigdal's Repositories
mcjmigdal/RNA-seq_data_analysis_course_for_biologists_may_2018
The goal of the course is to introduce basic RNA-seq data analysis, starting from experiment design and raw files to functional data analysis that can be performed using PC only. In brief, the content of the course will cover: general knowledge on RNA-seq library preparation (which kit/technology should I use and why? how many replicates? how deep should I sequence my samples?), quality check and filtering of the reads (including adapter trimming, rRNA removal), read alignment/quasi-mapping (can I perform read mapping on my PC without losing its specificity and efficacy?), performing gene counts (assigning reads to provided gene annotation), data normalization (which normalization types should I apply to my data?), differential expression data analysis, basic data visualization, functional analysis (GO terms, pathway analysis).
mcjmigdal/sumsamstats
summarising outputs of samtools stats with ATAC-seq qc in mind
mcjmigdal/macs2_replicates
Calling peaks with macs2 and combining infromation from replicates using Fisher method
mcjmigdal/scripts
Usefull scripts
mcjmigdal/shiitake
shiitake mini-project
mcjmigdal/.doom.d
mcjmigdal/alpine-simple-db
MariaDB running on Alpine Linux with included data [Docker]
mcjmigdal/bioinfo21
Bioinformatics Contest 2021
mcjmigdal/bionanno-notatki
mcjmigdal/biopython
Official git repository for Biopython (originally converted from CVS)
mcjmigdal/BITFAM_zebrafish
BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.
mcjmigdal/ConnectOR
multiple Species Orthology Finder
mcjmigdal/ehahelper
Helper function for Event history analysis, including tidying functions for coxme
mcjmigdal/fishfacts
Following hypermodern-python guide
mcjmigdal/getcoordinates_gaussian
Bash script to extract coordinates of optimized structure from GAUSSIAN log file
mcjmigdal/HPC_Ansible
Files for HPCKP15 Ansible hands-on session
mcjmigdal/makePlasmid
Pipeline for de-novo plasmid assembly from pair-end short reads. Reads are trimmed with Cutadapt, assembled with SPAdes.
mcjmigdal/mcjmigdal.github.io
mcjmigdal/mock.RPi.GPIO
Package provide mock version of RPi.GPIO library that can be used for developing on non-RPi devices.
mcjmigdal/naive_bayes_mixed_features
Exploring sklearn pipelines while implementing Naive Bayes with mixed type features
mcjmigdal/nand2tetris
mcjmigdal/profile2pwm
convert homer motif to pwm
mcjmigdal/pyHeart4Fish
A heart beat analysis tool for zebrafish hearts
mcjmigdal/pypath
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
mcjmigdal/rosalind
my solutions to rosalind problems
mcjmigdal/scrapeORCID
Get publication list from ORCID.
mcjmigdal/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
mcjmigdal/weather-station-esp32
Weather station build around BME280 sensor using ESP32 and E-Ink display
mcjmigdal/xcoredata
data package for github.com/bkaczkowski/xcore