Jacob Schreiber (@jmschrei)
github

jmschrei

Twitter logo Share LinkedIn logo Share Facebook logo Share

Top repositories

1

pomegranate

Fast, flexible and easy to use probabilistic modelling in Python.
Python
3,194
star
2

apricot

apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly. See the documentation page: https://apricot-select.readthedocs.io/en/latest/index.html
Jupyter Notebook
480
star
3

yahmm

Yet Another Hidden Markov Model repository.
Python
249
star
4

avocado

Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.
Jupyter Notebook
112
star
5

torchegranate

A temporary repository hosting a pomegranate re-write using PyTorch as the backend.
Jupyter Notebook
69
star
6

ledidi

Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
Jupyter Notebook
54
star
7

tfmodisco-lite

A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
Python
51
star
8

notebooks

Various notebooks and tutorials on subjects of interest.
Jupyter Notebook
36
star
9

PyPore

Tools used to analyze data from nanopore-based experiments.
Python
26
star
10

dragonnfruit

A method for analyzing scATAC-seq experiments.
Python
23
star
11

rambutan

Prediction of the 3D structure of the genome through statistically significant Hi-C contacts.
Jupyter Notebook
21
star
12

bpnet-lite

This repository hosts a minimal version of a Python API for BPNet.
Python
12
star
13

constraint_graphs

Repository for the data and associated notebook for the manuscript "Finding the optimal Bayesian network given a constraint graph."
Jupyter Notebook
6
star
14

antz

Bioinformatic tools for biologists, made pythonic!
Python
4
star
15

bam2bw

A command-line tool for reading SAM/BAM files and converted them directly to bigwig files.
Python
2
star
16

yabn

Yet Another Bayesian Network
Python
2
star
17

jmschrei.github.io

HTML
1
star
18

Abada

GUI for analyzing nanopore data, based on the Abada package.
Python
1
star
19

discern

Python
1
star
20

kiwano

Kiwano implements an approach for prioritizing epigenomic and transcriptomic characterization based on submodular selection and imputed experiments
Python
1
star