Diane Trout's repositories
woldlab-rna-seq
ENCODE3/4 bulk (port) and single-cell implementation of an illumina RNA-seq pipleine
igvf-seq-spec-demo
Example notebook for creating and attaching seq-spec files to IGVF fastq files.
y2ave_seqspecs
Work in progress seqspecs for Y2AVE processing for IGVF
conda-recipes
packaging some software needed for my snakemake workflows that use conda based wrappers
seqspec
machine-readable file format for genomic library sequence and structure
guix-detrout
Staging repository for me to package things I find useful using Guix.
htsworkflow
Wold lab LIMS
mex_gene_archive
Utilities to handle an archive of matrix market exchange count files as frequently generated by single cell gene mappers
debian-spp
Debian packaging for spp
encode4-curation
notes for submiting things for ENCODE4 project
igvf_mice
Database for tracking biosamples and processed result files for our joint UCI/Caltech IGVF project
LR-splitpipe
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
encoded_client
Search and submit to the ENCODE-DCC portal.
woldrnaseq-wrappers
Snakemake wrappers used by woldlab-rna-seq project
encode4-rna-wg-paper
Python notebooks supporting ENCODE4 RNA working group paper
nextcloud-news
:newspaper: RSS/Atom feed reader
all-positive-integers-in-ascending-order
A list of all positive integers in ascending order (incomplete)
dask
Parallel computing with task scheduling
apparmor-det
Apparmor security profiles
TALON
Technology agnostic long read analysis pipeline for transcriptomes
mumo
mumo is the Mumble Moderator framework which simplifies development of plugins connecting to a Mumble server via Ice. mumo handles basic ICE connectivity and contains basic module loading and message multiplexing.
hello-actions
Repository to investigate github actions
encode3-curation
Various work in progress files working on trying to curate our ENCODE data submissions.
debian-guix
Debian packaging recipe for Guix package manager
mythtv
The official MythTV repository
scaqmd_sensor
home-assistant sensor to watch South Coast AQMD's AQI and Forecast