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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 CCAconcordex
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 Bioinformaticsbcl2fastq
source code for bcl2fastq2, files from illuminaCP_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
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