There are no reviews yet. Be the first to send feedback to the community and the maintainers!
gget
๐งฌ gget enables efficient querying of genomic reference databaseskallisto
Near-optimal RNA-Seq quantificationffq
A tool to find sequencing data and metadata from public databases.BI-BE-CS-183-2023
Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023sleuth
Differential analysis of RNA-Seqposeidon
poseidon system - open source syringe pumps and microscope for laboratorieskb_python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processingkallistobustools
kallisto | bustools workflow for pre-processing single-cell RNA-seq dataseqspec
machine-readable file format for genomic library sequence and structurevoyager
From geospatial to spatial -omicspicasso
Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.scRNA-Seq-TCC-prep
Preprocessing of single-cell RNA-Seq (deprecated)metakallisto
Using kallisto for metagenomic analysisLP_2021
kallisto-transcriptome-indices
Reference transcriptome indices build from kallisto for popular organismssircel
Identify cell barcodes from single-cell genomics sequencing experimentsSpatialFeatureExperiment
Extension of SpatialExperiment with sfMCML
kallisto_paper_analysis
Analysis from kallisto paperNYMP_2018
kma
Keep Me Around: Intron Retention Detectionmonod
The Monod package fits CME models to sequencing data.gget_examples
Examples for gget (https://github.com/pachterlab/gget).colosseum
colosseum system - open source fraction collector for laboratoriesGFCP_2022
RNA velocity validationMBGBLHGP_2019
Code for reproducing results from the paper "Modular and efficient pre-processing of single-cell RNA-seq data"BBB
Bioinformatics for Benched BiologistsBHGP_2022
kite
kallisto index tag extractoraggregationDE
Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachterqcbc
splitcode
Flexible and efficient parsing, interpreting and editing of sequencing readsPCCA
Code for performing PCA followed by CCAsleuth_paper_analysis
Code to reproduce analyses from the sleuth paperconcordex
Identification of spatial homogeneous regionsRMEJLBASBMP_2024
Repository for the paper "The impact of package selection and versioning on single-cell RNA-seq analysis"CGCCP_2023
scVI extension for unspliced RNACBP_2021
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".SBP_2019
Code for producing the analysis in the "Quantifying the tradeoff between sequencing depth and cell number in single-cell RNA-seq" manuscriptvoyagerpy
bears_analyses
Examples of kallisto + sleuthGSP_2019
Code for reproducing results from the paper "RNA velocity and protein acceleration from single-cell multiomics experiments."kallisto-sleuth-workshop-2016
materials and website for the 2016 kallisto sleuth workshoplair
home of the bear's lairsleuth_walkthroughs
Some sleuth walkthroughs to help you get startedscATAK
concordexR
Compute the neighborhood consolidation matrix and identify SHRsMBLGLMBHGP_2021
Bi-BE-CS-183-2022
Website for the 2021-2022 Caltech class Bi/BE/CS 183: Introduction to Computational Biology and BioinformaticsCP_2023
bam2tcc
voyager-testing
GVP_2023
scRNA-seq, regulation, and sysbiomonod_examples
Tutorials for the Monod package, which fits CME models to sequencing data.BGP_2023
biophysics
Repository for Pachter Lab Biophysicsmuseumst
Museum of Spatial TranscriptomicsGCCP_2022
SGYP_2019
BLCSBGLKP_2020
Code for analysis of SARS-CoV-2 sequencing based diagnostic testing datakallisto-D
zika
sleuth workflow for processing zika RNA-seq datasetSHSOHMP_2024
Code for reproducing the results in the second version of the preprint "Accurate quantification of single-nucleus and single-cell RNA-seq transcripts"LP_2024
GBP_2024
pegasus
modular stepper motor control with Arduino, CNC motor sheild, and Pololu stepper driver. also the workhorse of poseidon and colosseumSP_2019
GVFP_2021
SDE comparison preprintCOVID19-County
COVID-19 data from LA CountyBGP_2024
FGP_2024
HSHMP_2022
bibecs183
Bi/BE/CS 183 Winter 2019 - Introduction to Computational Biology and BioinformaticsAAQuant
Annotation-Agnostic RNA-seq QuantificationBSP_2023
BP_2020_2
log(x+1) and log(1+x)CP_2021
Code for reproducing the results in "The Split Senate" paperGRNP_2020
Repository for reproducing the results and figures in Gustafsson et al. 2020BKMGP_2021
isolate_transcripts
CWGFLHGCCHAP_2021
DBALLSMRDMCMGWSTPMBDKPFP_2023
GP_2020
Code to reproduce results in the paper "Special Function Methods for Bursty Models of Transcription"SFEData
Example SpatialFeatureExperiment datasetsPROBer
PROBer: A general toolkit for analyzing sequencing-based โtoeprintingโ assaysBTRBP_2020
BP_2020
Decrease in ACE2 mRNA expression in aged mouse lung, bioRxiv, 2020.GP_2021_4
CGP_2024_2
HPM_2022
Simulations of the robustness of AAQuant to noiseYLMP_2018
Scripts to reproduce analysis in YLMP, 2018bcltools
(still in development only a few things work) tools for converting bcls to fastqs and fastqs to bclseXpress
Streaming fragment assignment for real-time analysis of sequencing experimentsmake
Open source bioinstrumentation projectsGPCTP_2019-2
GP_2020_2
Intrinsic/extrinsic noise mini-projectGP_2021_3
kallisto_tests
A set of (regression) tests for kallistoKBP_2023
Love Open Source and this site? Check out how you can help us