mcjmigdal Goto Github PK

.doom.d

alpine-simple-db

MariaDB running on Alpine Linux with included data [Docker]

bioinfo21

Bioinformatics Contest 2021

bionanno-notatki

biopython

Official git repository for Biopython (originally converted from CVS)

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.

connector

multiple Species Orthology Finder

ehahelper

Helper function for Event history analysis, including tidying functions for coxme

fishfacts

Following hypermodern-python guide

getcoordinates_gaussian

Bash script to extract coordinates of optimized structure from GAUSSIAN log file

hpc_ansible

Files for HPCKP15 Ansible hands-on session

macs2_replicates

Calling peaks with macs2 and combining infromation from replicates using Fisher method

makeplasmid

Pipeline for de-novo plasmid assembly from pair-end short reads. Reads are trimmed with Cutadapt, assembled with SPAdes.

mcjmigdal.github.io

mock.rpi.gpio

Package provide mock version of RPi.GPIO library that can be used for developing on non-RPi devices.

naive_bayes_mixed_features

Exploring sklearn pipelines while implementing Naive Bayes with mixed type features

nand2tetris

profile2pwm

convert homer motif to pwm

pyheart4fish

A heart beat analysis tool for zebrafish hearts

pypath

Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

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).

rosalind

my solutions to rosalind problems

scrapeorcid

Get publication list from ORCID.

scripts

Usefull scripts

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

shiitake

shiitake mini-project

sumsamstats

summarising outputs of samtools stats with ATAC-seq qc in mind

weather-station-esp32

Weather station build around BME280 sensor using ESP32 and E-Ink display

xcoredata

data package for github.com/bkaczkowski/xcore