Pinello Lab (@pinellolab)
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pinellolab

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Top repositories

1

DNA-Diffusion

๐Ÿงฌ Generative modeling of regulatory DNA sequences with diffusion probabilistic models ๐Ÿ’จ
Python
363
star
2

CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
Python
272
star
3

STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
Jupyter Notebook
166
star
4

scATAC-benchmarking

Benchmarking computational single cell ATAC-seq methods
Jupyter Notebook
161
star
5

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis
Python
105
star
6

simba

SIMBA: SIngle-cell eMBedding Along with features
Python
54
star
7

haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
HTML
43
star
8

AmpUMI

Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
Python
41
star
9

pyrovelocity

๐’ซrobabilistic modeling of RNA velocity โฌฑ
Python
40
star
10

GRAFIMO

GRAph-based Finding of Individual Motif Occurrences
Python
27
star
11

pychromVAR

A python package for chromVAR
Python
26
star
12

CRISPRitz

Tool package to perform in-silico CRISPR analysis and assessment
Python
21
star
13

CRISPR-SURF

Python
16
star
14

PrimeDesign

Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!
Python
14
star
15

singlecellvr

HTML
13
star
16

CRISPRme

Python
11
star
17

MotifRaptor

Explore the effect of genetic variants on transcription factor binding sites
Python
8
star
18

STREAM2

STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics data
Python
8
star
19

crispr-bean

Base Editing screens' Activity-Normalized variant effect size estimation
Python
8
star
20

CRISPRlungo

Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements
Python
5
star
21

perturbvelo

Python
5
star
22

SVG_Benchmarking

Benchmarking methods for identification of spatially variable genes
Jupyter Notebook
3
star
23

MEGATRON

MEGA TRajectories of clONes
Python
3
star
24

bean_manuscript

Scripts for plots used in manuscript
Jupyter Notebook
3
star
25

STREAM_web

STREAM interactive website stream.pinellolab.org
Python
2
star
26

simba_pbg

A customized PyTorch-BigGraph (PBG) package for "simba", modified from https://github.com/facebookresearch/PyTorch-BigGraph
Python
2
star
27

simba_comparison

Scripts used for performance comparison in SIMBA manuscript.
Jupyter Notebook
2
star
28

simstpy

A framework for simulation of spatially-resolved omics data using python
Jupyter Notebook
2
star
29

screen-simulation

Simulate bulk CRISPR screen, sorting or proliferation, with and reproter/target edits
Python
2
star
30

pbl-comparison-study

Comparison of probablisitc programming languages in Python: PyStan, PyMC3, Edward, and Pyro
Jupyter Notebook
1
star
31

STREAM_atac

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data. Preprocessing steps for single cell atac-seq data
Python
1
star
32

perturb-tools

Analysis Framework for Pooled CRISPR Genome Editing Screens
Jupyter Notebook
1
star
33

CRISPR_WGS_Detection

Jupyter Notebook
1
star