Hi-C spectral decomposition workflow

Spectral decomposition for characterizing long-range interaction profiles in Hi-C maps. Snakemake workflow for the unsupervised method presented in Spracklin, Abdennur et al., 2021. Steps Place supplementary bigwig file information in config/track_metadata.tsv to include in graphical outputs. Must be tab-delimited, including header. Must have columns: Name: a display name ID: a unique identifier to use in the database (can be the same as Name) FileFormat: must be the string bigWig Path: a local path to the file Edit config.yaml. Run: # […]

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An Alfred workflow to restore iTerm2 window Arrangements

This alfred workflow will list avaliable iTerm2 arrangements and let you select one to restore. Requirements iterm2: Build 3.4.15 (not tested on other versions but myght work) And the following python libraries: pip3 install iterm2 pip3 install pyobjc This workfllow will use the python from iterm2 on ~/Library/ApplicationSupport/iTerm2/Scripts/get_window_arrangements/iterm2env/versions/3.8.6/bin/python3 Usage Just type iTermA on alfred and it will: Launch iterm2 if its closed List the avaliable window arrangements Restore the selected window arrangement Download Check the releases page to download it. […]

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Collection of useful command line utilities and snippets to help you organise your workspace and improve workflow

Utility library Scripts To install scripts into your bin folder, simply run: Note that this requires you to either add ~/.local/bin to path, or specify a custom bin path (e.g. sudo python install.py /usr/bin). This will simply copy all scripts to that directory without their .py extension. Clone If you ever needed to quickly clone 3rd party git repositories or simply structure your current repositories, you’ll definitely find this utility useful. This utility allows you to automatically organise your repositories […]

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A fork of the BakeTool with some improvements that I did to have better workflow

This is a fork of the BakeTool with some improvements that I did to have better workflow. 99.99% of work was done by BakeTool team. But as there is no public git repository and as it was hard for me to contact the team with my bug-fixes and extra features, I decided to setup this repo. I think, that Blender baking workflow, as it is without any add-ons, is the worst, that can be imagined. At least, I can’t imagine […]

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AI and Machine Learning workflows on Anthos Bare Metal

AI and Machine Learning workflows using TensorFlow on Anthos Bare Metal. TensorFlow is one of the most popular ML frameworks (10M+ downloads per month) in use today, but at the same time presents a lot of challenges when it comes to setup (GPUs, CUDA Drivers, TF Serving etc), performance tuning, cluster provisioning, maintenance, and model serving. This work will showcase the easy to use guides for ML model serving, training, infrastructure, ML Notebooks, and more on Anthos Bare Metal. Terraform […]

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Python client for using Prefect Cloud with Saturn Cloud

prefect-saturn prefect-saturn is a Python package that makes it easy to run Prefect Cloud flows on a Dask cluster with Saturn Cloud. For a detailed tutorial, see “Fault-Tolerant Data Pipelines with Prefect Cloud “. Installation prefect-saturn is available on PyPi. pip install prefect-saturn prefect-saturn can be installed directly from GitHub pip install git+https://github.com/saturncloud/[email protected] Getting Started prefect-saturn is intended for use inside a Saturn Cloud environment, such as a Jupyter notebook. import prefect from prefect import Flow, task from prefect_saturn import […]

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