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basicpythonforbeginners

I see a lot of biologists who are willing to learn python. However, it's really difficult to get started. I went through same stage and I am trying to support these biologist with very simple queries yet takes a lot of time because of lack of skills to even properly do stack or google. I will mainly focus on the LinkedIn users. I will also try to add functions for people who want to do something for their project based on suggestions. I also encourage others to contribute if they want to.

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

coin_flip_game

Used to illustrate why bagging is effective

conga

Clonotype Neighbor Graph Analysis

doc-annovar

Documentation for the ANNOVAR software

flowkit

A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces

folder-structure-conventions

Folder / directory structure options and naming conventions for software projects

ftd_prodia

Analysis of proteomics data of FTD subtypes

gseapy

Gene Set Enrichment Analysis in Python

gt-cnn

GT fold classification

jump

jump-ptm

jumpg

Proteogenomics Software

jumpspeclib

This is a spectral library generation, search, filter and quantification suite for TMT labeled MS data.

linkedin_friends

machinelearningwithpython

maxfuse

moff

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file

muon-tutorials

Tutorials for multimodal omics data analysis

projectils

Interpretation of cell states using reference single-cell maps

rna_seq_gsea_py

This is post rna seq analysis to see the clusters

sanbomics_scripts

scripts and notebooks from sanbomics

scatacseq-analysis-notes

my notes for scATACseq analysis

scgpt

scGPT nature methods paper

scpml

scrna-seq-workshop-fall-2019

Harvard FAS informatics scRNAseq workshop website

scrna-seq_online

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

tn_test

post-clustering differential expression test