Pinned Repositories
13_deft
Code for "Rapid and Rapid and deterministic estimation of probability densities using scale-free field theories" arXiv:1312.6661 [physics.data-an]
14_crispr
Code and processed data reported in Shi et al. (2015) Nat. Biotechnol. [in press]
14_maxent
Code for "Unification of Field Theory and Maximum Entropy Methods for Learning Probability Densities" (2014) by Justin B. Kinney, available at http://arxiv.org/abs/1411.5371
16_titeseq
Processed data and analysis code for Adams et al., 2016 bioRxiv
18_urp
Excercises for the 2018 URP programming workshop
24e_qbbootcamp
Repository for the 2024 QB Bootcamp
24e_urp
Code for the 2024 CSHL URP Python Programming Course
logomaker
Software for the visualization of sequence-function relationships
mavenn
MAVE-NN: genotype-phenotype maps from multiplex assays of variant effect
suftware
SUFTware: Statistics Using Field Theory
jbkinney's Repositories
jbkinney/logomaker
Software for the visualization of sequence-function relationships
jbkinney/mavenn
MAVE-NN: genotype-phenotype maps from multiplex assays of variant effect
jbkinney/suftware
SUFTware: Statistics Using Field Theory
jbkinney/18_urp
Excercises for the 2018 URP programming workshop
jbkinney/13_deft
Code for "Rapid and Rapid and deterministic estimation of probability densities using scale-free field theories" arXiv:1312.6661 [physics.data-an]
jbkinney/15_splicing
jbkinney/22e_qbbootcamp
Materials for the 2022 QB Bootcamp at Cold Spring Harbor Laboratory
jbkinney/19_mlcb
Code for Tareen & Kinney (MLCB 2019) https://doi.org/10.1101/835942
jbkinney/23e_qbbootcamp
2023 Quantitative Biology Bootcamp at Cold Spring Harbor Laboratory
jbkinney/24e_urp
Code for the 2024 CSHL URP Python Programming Course
jbkinney/21_nickels
Computational Scripts for Transcriptional Pausing
jbkinney/22_drugs
22_drugs
jbkinney/22e_urp
2021 URP Python course at CSHL
jbkinney/23e_urp
Code for the 2023 CSHL URP Python Programming Course
jbkinney/24e_qbbootcamp
Repository for the 2024 QB Bootcamp
jbkinney/17_ars
Analysis code for Hu et al., 2020
jbkinney/17_inducibility
Supplemental Code for Forcier et al., 2018
jbkinney/18_expressionmanifolds
Data and analysis scripts for Forcier et al., 2018 (preprint)
jbkinney/18_qbbootcamp
Code for the 2018 QB Bootcamp in the Watson School for Biological Sciences
jbkinney/18_qbcourse
jbkinney/19_qbbootcamp
GitHub repository for the 2019 QB Bootcamp
jbkinney/19_urp
Materials for the 2019 URP Programming and Data Analysis Course at Cold Spring Harbor Laboratory
jbkinney/19_urp_staging
Exercises for the 2019 URP Python Programming and Data Analysis Course
jbkinney/20_nickels
jbkinney/20_qbbootcamp
Repository for the 2020 QB Bootcamp, CSHL School of Biological Sciences
jbkinney/21_qbbootcamp
Repository for the 2021 QB Bootcamp at CSHL
jbkinney/23_posfai
jbkinney/gitignore
A collection of useful .gitignore templates
jbkinney/MaveReferences
Table of Multiplexed Assay of Variant Effect (MAVE) studies
jbkinney/old_21_qbbootcamp