adeslatt
https://orcid.org/0000-0001-7951-3439 PhD Tumor Biology, MSc Computer Science, BSc Mathematics solving biological questions at scale in the cloud
Science and Technology Consulting LLC
Pinned Repositories
cDNA-cupcake-docker
This is the repository for the Dockerfile made to containerize and make the package available for the tools in https://github.com/Magdoll/cDNA_Cupcake. The package is automatically built and pushed upon any push to the repository using GitHub actions.
drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
Kids-First-Elements-of-Style-Workflow-Creation-Maintenance
post-rmats-single-run
post-rmats-single-run
rmats-ijc-analysis
rmats-ijc-analysis
sync-seq
A Nextflow workflow encapsulating the computational components to take output from the 15:1 molar libraries of gDNA:cDNA sequenced on the PacBio Revio following the protocols published in "Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition".
Elements-of-Style-Reproducible-Workflow-Creation-Maintenance-Tutorial
dry-bench-skills-for-researchers
Learning resources originally for a class held December 2020 "Dry bench skills for Researchers". Expanding based upon mini-courses.
sbas
CloudOS Digital Research Environment
splicing-pipelines-nf
Repository for the Anczukow-Lab splicing pipeline
adeslatt's Repositories
adeslatt/drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
adeslatt/2018-11-01-teacherCarpentryExample
adeslatt/atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
adeslatt/BioEditMultiSequenceAlignment
Resurrecting multiple sequence alignment method used to analyze long read RNAsequencing data from PacBIo on Healthy Human Bone Marrow -- it begins with calling the open reading frames to translate the DNA to Protein sequence and ends with at time manual editing to align the sample specific sequence data.
adeslatt/BioITHackathons-FAIRAssessment2018JaxTeam
adeslatt/BioITWorld2019FAIRApplications
adeslatt/boneMarrowComparsions
utilities to do analysis and comparisons between groups
adeslatt/computational-skills-for-the-researcher
Collection of classes offered - providing instruction surrounding community based workflows, such as nextflow as well as offering insights in using JupyterLab notebooks to perform analyses and generate publication ready figures.
adeslatt/google-sheet-to-github-website
This is a working project for publishing data to Github Pages using Google Spreadsheet as the data source.
adeslatt/human-testdata
testdata
adeslatt/ideas
Tracking of thoughts and ideas for projects, science advancing and what will get us to solving the problems we want to be solving
adeslatt/ISOSeqNeoAntigen-nf
The scripts to go from PacBio ISOSeq reads to NeoAntigen with HLA-typing for patient specific neo-antigen discovery
adeslatt/jax-tutorial
Tutorial for Jackson Labs intro to Nextflow, containers, FlowCraft and Deploit
adeslatt/methylSeqCaptureSeq
Megan Barefoot's PhD thesis project
adeslatt/NN_Pseudobs
On the use of neural networks for survival models with censored data
adeslatt/pacBioUtilityPrograms
Sets of routines useful from Liz Tseng
adeslatt/Peptides-SpecTra-Annotations-PaSTA
an analysis workflow to generate annotated peptide sequence from proteomic spectra using containerized tools.
adeslatt/RIT_retreat_CICD
Examples for git/devops lesson on March 11, 2020
adeslatt/rMATS-STAT
adeslatt/rmats4
Docker container for rmats 4.0.2 and R 3.6.0
adeslatt/sarek
Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing
adeslatt/sbas-nf
mirrored version of cgpu/sbas-nf
adeslatt/sbas_gtf
This repository contains the results of the scanning of gencode.v30 by rMATS 3.2.5.
adeslatt/sbas_test
adeslatt/Single-cell-RNA-seq-data-analysis-2018
Event page: https://www.csc.fi/web/training/-/single-cell-rnaseq-r-2018
adeslatt/Slide-Carousel-Simple
simple slide carousel / photo viewer
adeslatt/splicing-nf-container
Container for tools needed for the nextflow splicing-pipeline-nf
adeslatt/staries
The *ies. A series of <star>-ies util snippets, scripts or templates that I use day to day.
adeslatt/TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
adeslatt/wgbs_tools
tools for working with WGBS data while preserving reads intrinsic dependencies