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Open source bioinstrumentation projects

gget

🧬 gget enables efficient querying of genomic reference databases

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kallisto

Near-optimal RNA-Seq quantification

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ffq

A tool to find sequencing data and metadata from public databases.

Python

538

BI-BE-CS-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

Jupyter Notebook

389

sleuth

Differential analysis of RNA-Seq

305

poseidon

poseidon system - open source syringe pumps and microscope for laboratories

Jupyter Notebook

168

kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

Python

141

kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

114

seqspec

machine-readable file format for genomic library sequence and structure

Python

108

voyager

From geospatial to spatial -omics

picasso

Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.

Jupyter Notebook

scRNA-Seq-TCC-prep

Preprocessing of single-cell RNA-Seq (deprecated)

Jupyter Notebook

metakallisto

Using kallisto for metagenomic analysis

Python

LP_2021

TeX

kallisto-transcriptome-indices

Reference transcriptome indices build from kallisto for popular organisms

sircel

Identify cell barcodes from single-cell genomics sequencing experiments

Jupyter Notebook

SpatialFeatureExperiment

Extension of SpatialExperiment with sf

MCML

Python

kallisto_paper_analysis

Analysis from kallisto paper

HTML

NYMP_2018

Jupyter Notebook

kma

Keep Me Around: Intron Retention Detection

Python

monod

The Monod package fits CME models to sequencing data.

Python

gget_examples

Examples for gget (https://github.com/pachterlab/gget).

Jupyter Notebook

GFCP_2022

RNA velocity validation

Jupyter Notebook

MBGBLHGP_2019

Code for reproducing results from the paper "Modular and efficient pre-processing of single-cell RNA-seq data"

Jupyter Notebook

colosseum

colosseum system - open source fraction collector for laboratories

Jupyter Notebook

BBB

Bioinformatics for Benched Biologists

Jupyter Notebook

BHGP_2022

Jupyter Notebook

kite

kallisto index tag extractor

Python

aggregationDE

Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter

qcbc

Jupyter Notebook

splitcode

Flexible and efficient parsing, interpreting and editing of sequencing reads

PCCA

Code for performing PCA followed by CCA

Python

sleuth_paper_analysis

Code to reproduce analyses from the sleuth paper

concordex

Identification of spatial homogeneous regions

Python

RMEJLBASBMP_2024

Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"

Jupyter Notebook

CGCCP_2023

scVI extension for unspliced RNA

Jupyter Notebook

CBP_2021

Jupyter Notebook

BYVSTZP_2020

This repository contains the code for reproducing all the results and figures from the preprint "Isoform specificity in the mouse primary motor cortex".

Jupyter Notebook

SBP_2019

Code for producing the analysis in the "Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq" manuscript

Jupyter Notebook

bears_analyses

Examples of kallisto + sleuth

Python

voyagerpy

Python

GSP_2019

Code for reproducing results from the paper "RNA velocity and protein acceleration from single-cell multiomics experiments."

Jupyter Notebook

kallisto-sleuth-workshop-2016

materials and website for the 2016 kallisto sleuth workshop

CSS

lair

home of the bear's lair

CSS

sleuth_walkthroughs

Some sleuth walkthroughs to help you get started

HTML

scATAK

Jupyter Notebook

concordexR

Compute the neighborhood consolidation matrix and identify SHRs

MBLGLMBHGP_2021

Jupyter Notebook

Bi-BE-CS-183-2022

Website for the 2021-2022 Caltech class Bi/BE/CS 183: Introduction to Computational Biology and Bioinformatics

Jupyter Notebook

bcl2fastq

source code for bcl2fastq2, files from illumina

CP_2023

bam2tcc

voyager-testing

GVP_2023

scRNA-seq, regulation, and sysbio

Jupyter Notebook

monod_examples

Tutorials for the Monod package, which fits CME models to sequencing data.

Jupyter Notebook

BGP_2023

Jupyter Notebook

biophysics

Repository for Pachter Lab Biophysics

Python

museumst

Museum of Spatial Transcriptomics

GCCP_2022

Roff

SGYP_2019

Jupyter Notebook

BLCSBGLKP_2020

Code for analysis of SARS-CoV-2 sequencing based diagnostic testing data

Jupyter Notebook

kallisto-D

zika

sleuth workflow for processing zika RNA-seq dataset

HSSOHMP_2024

Code for reproducing the results in the second version of the preprint "Accurate quantification of single-nucleus and single-cell RNA-seq transcripts"

C++

GBP_2024

Jupyter Notebook

pegasus

modular stepper motor control with Arduino, CNC motor sheild, and Pololu stepper driver. also the workhorse of poseidon and colosseum

Python

SP_2019

Jupyter Notebook

GVFP_2021

SDE comparison preprint

Jupyter Notebook

COVID19-County

COVID-19 data from LA County

LP_2024

BGP_2024

HSHMP_2022

bibecs183

Bi/BE/CS 183 Winter 2019 - Introduction to Computational Biology and Bioinformatics

Jupyter Notebook

AAQuant

Annotation-Agnostic RNA-seq Quantification

C++

BSP_2023

Jupyter Notebook

FGP_2024

Jupyter Notebook

BP_2020_2

log(x+1) and log(1+x)

Jupyter Notebook

CP_2021

Code for reproducing the results in "The Split Senate" paper

Python

GRNP_2020

Repository for reproducing the results and figures in Gustafsson et al. 2020

BKMGP_2021

isolate_transcripts

CWGFLHGCCHAP_2021

DBALLSMRDMCMGWSTPMBDKPFP_2023

Jupyter Notebook

GP_2020

Code to reproduce results in the paper "Special Function Methods for Bursty Models of Transcription"

MATLAB

SFEData

Example SpatialFeatureExperiment datasets

PROBer

PROBer: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays

C++

BTRBP_2020

Jupyter Notebook

BP_2020

Decrease in ACE2 mRNA expression in aged mouse lung, bioRxiv, 2020.

Jupyter Notebook

GP_2021_4

HTML

CGP_2024_2

Jupyter Notebook

HPM_2022

Simulations of the robustness of AAQuant to noise

YLMP_2018

Scripts to reproduce analysis in YLMP, 2018

Shell

bcltools

(still in development only a few things work) tools for converting bcls to fastqs and fastqs to bcls

Python

eXpress

Streaming fragment assignment for real-time analysis of sequencing experiments

GPCTP_2019-2

GP_2020_2

Intrinsic/extrinsic noise mini-project

Jupyter Notebook

GP_2021_3

Jupyter Notebook

kallisto_tests

A set of (regression) tests for kallisto

100

KBP_2023

pachterlab/make

pachterlab

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