thyagoleal
Molecular biology | bioinformatics | programming.
Innovative Genomics Institute, UC BerkeleyBerkeley, California, USA
Pinned Repositories
2019_scWorkshop
Repo for Physalia course Analysis of Single Cell RNA-Seq data
cpulimit
CPU usage limiter for Linux
Intro-to-rnaseq-hpc-O2
This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
leprosy_reanalysis_paper
R code used to reanalyze/integrate/visualize a set of 9 leprosy public microarray datasets
mleprae-genomics_workflow
Snakemake workflow for processing Mycobacterium leprae whole genome sequencing data
qPCR-Biomark
Biomark Fluidigm qPCR data set: processing and analysis
scRNA_Lep
thyagoleal.github.io
Landing page
thyagoleal's Repositories
thyagoleal/leprosy_reanalysis_paper
R code used to reanalyze/integrate/visualize a set of 9 leprosy public microarray datasets
thyagoleal/mleprae-genomics_workflow
Snakemake workflow for processing Mycobacterium leprae whole genome sequencing data
thyagoleal/thyagoleal.github.io
Landing page
thyagoleal/ADMIXTURE-smartPCA-PLINK-and-EIGENSOFT
Scripts and notes on how to analyse processed NGS data
thyagoleal/base-editor-design-tool
This tool designs guides for use with the base editor technology.
thyagoleal/EditR
EditR: an algorithm for simple and cost effective measurement of base editing by quantifying Sanger trace fluorescence
thyagoleal/enrichplot
Visualization of Functional Enrichment Result
thyagoleal/getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
thyagoleal/haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
thyagoleal/immunedeconv
A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter)
thyagoleal/indigo
Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products
thyagoleal/IntroductionToGenomics
Presentations from the "Introduction to Genomics" lecture series on the Genomics Boot Camp channel on YouTube.
thyagoleal/knock-knock
toolkit for analyzing genome editing experiments
thyagoleal/lab-mgmt
thyagoleal/land_page
Landing page source files
thyagoleal/LP_2021
thyagoleal/mac-setup
The commands and processes I run to setup a new Mac computer
thyagoleal/PrimeDesign
Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!
thyagoleal/RforMassSpectrometry.org
The R for Mass Spectrometry Initiative home page
thyagoleal/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
thyagoleal/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
thyagoleal/scRNA-seq_online
thyagoleal/seq2science
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
thyagoleal/snakemake-econ-r
reproducible research project template for R using Renv and snakemake with an econ application
thyagoleal/snakemake-workflow-template
A template for standard compliant snakemake-workflows
thyagoleal/statistical_inferences
Repository for the textbook 'Improving Your Statistical Inferences' by Daniel Lakens
thyagoleal/styles
Official repository for Citation Style Language (CSL) citation styles.
thyagoleal/thyagoleal
thyagoleal/variancePartition
Quantify and interpret divers of variation in multilevel gene expression experiments
thyagoleal/wf-clone-validation