rnaseq
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rnaseq | HomeBrew | |
---|---|---|
14 | 1278 | |
758 | 38,997 | |
4.9% | 1.6% | |
9.5 | 10.0 | |
6 days ago | 7 days ago | |
Nextflow | Ruby | |
MIT License | BSD 2-clause "Simplified" License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
rnaseq
- R pipelines for bulk RNA-seq analyses
- What are some good examples of well-engineered bioinformatics pipelines?
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Generate GUIs and deploy bioinformatics workflows with python
First lets recognize that the framework presented has new features that don't exist in the previous DSLs you mention. Many developers highly value these additions and they along could justify a new stab at a workflow language: and for many the represent tradeoff * Interface generation * Declarative cloud resource provisionment * Static typing * Native python support This workflow has a similar level of complexity to nf-core/rnaseq (not the same, but similar in number of constituent tasks for the purpose of counting transcript abundance). It ingests raw sequencing reads, runs QC + trimming, does psuedo-alignment, recovers counts from abundance estimates, and aggregates counts over a many samples for direct use by diff-exp tools. (It is not 'running salmon'. I think that is a reductionist take.) It does this in addition to dynamically building React.js interfaces, adding static type validation to input parameters, and deploying cloud infrastructure in a simpler way. For the lines of code comparison, I think it is a weird way to compare software as the number of lines of code is no proxy for legibility, ease of development, likelihood of long-term maintenance (many more people know python than nextflow). Nonetheless nf-core/rnaseq has nearly 1000 lines alone in its workflow entrypoint alone - https://github.com/nf-core/rnaseq/blob/master/workflows/rnaseq.nf . With imported modules + subworkflows, LOC actually reaches the many thousands.. (Now I understand it is more complex and mature, but I highlight why I think the comparison is weird and wonder what you are even comparing to.) Whereas the entire logic of the presented pipeline is actually neatly encapsulated in 1200 lines of a single file. Overall this feels like a that doesn't come from a place of rational discourse, rather group dislike for something new and different. What I would like to do is address and talk about specific technical points (preferably over issues on github) so conversations can be productive and improve the tools I am working on.
- I've been really frustrated with picking the right tools for bulk RNA-seq, so I did a long literature review and wrote this workflow
- Software repository and hackathons
- Introduction to RNAseq and microRNA?
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Tkinter for python 3.10 broken on MacOS?
Not really sure why it's a problem for you, I'm working on rnaseq and they use a very big input dataset, also outputs huge datasets too. It uses docker so you can deploy fast on VMs.
HomeBrew
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Tools for Linux Distro Hoppers
Hopping from one distro to another with a different package manager might require some time to adapt. Using a package manager that can be installed on most distro is one way to help you get to work faster. Flatpak is one of them; other alternative are Snap, Nix or Homebrew. Flatpak is a good starter, and if you have a bunch of free time, I suggest trying Nix.
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SQLite Schema Diagram Generator
Are you using SQLite that ships with macOS, or SQLite installed from homebrew?
I had a different problem in the past with the SQLite that ships with macOS, and have been using SQLite from homebrew since.
So if it’s the one that comes with macOS that gives you this problem that you are having, try using SQLite from homebrew instead.
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Perfect Elixir: Environment Setup
I’m on MacOS and erlang.org, elixir-lang.org, and postgresql.org all suggest installation via Homebrew, which is a very popular package manager for MacOS.
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You're Installing Node.js Wrong. That's OK, Here Is How To Fix It 🙌
I have always either installed Node from the installer provided by the Nodejs website or, via Brew in macOS. I have also used nvm in the past but did not know that there was a best practice to guide us.
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Test Driving a Rails API - Part One
A running Rails application needs a database to connect to. You may already have your database of choice installed, but if not, I recommend PostgreSQL, or Postgres for short. On a Mac, probably the easiest way to install it is with Posrgres.app. Another option, the one I prefer, is to use Homebrew. With Homebrew installed, this command will install PostgreSQL version 16 along with libpq:
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Effective Neovim Setup. A Beginner’s Guide
On a macOS machine, you can use homebrew by running the command.
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Radicle: Open-Source, Peer-to-Peer, GitHub Alternative
This is an overreaction, almost to the point of absurdity.
Risks inherent to pipe installers are well understood by many. Using your logic, we should abandon Homebrew [1] (>38k stars on GitHub), PiHole [2] (>46k stars on GitHub), Chef [3], RVM [4], and countless other open source projects that use one-step automated installers (by piping to bash).
A more reasonable response would be to coordinate with the developers to update the docs to provide alternative installation methods, rather than throwing the baby out with the bathwater.
[1] https://brew.sh/
[2] https://github.com/pi-hole/pi-hole
[3] https://docs.chef.io/chef_install_script/#run-the-install-sc...
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I'm confused: what's with the project descriptions at HTTPS://pkgx.dev/pkgs/?
And by supercookie, do you mean this UUID? https://github.com/Homebrew/brew/commit/57844530a94d5686029c...
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How To Set Up Your Coding Environment
On a Mac, do not use HomeBrew to install NVM. The NVM project recommends using their script. We had a few issues using NVM installed through HomeBrew over the years — issues we did not have when using their installer script.
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Ask HN: Trouble with a Stargate
I'm sorry to be asking this as I find it a bit silly, but it's blocking my PR [3], so could a few of you star the project on Github [1] to get my PR to run?
[1] https://github.com/laktak/chkbit-py
[2] https://brew.sh
[3] https://github.com/Homebrew/homebrew-core/pull/160018
What are some alternatives?
spack - A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
asdf - Extendable version manager with support for Ruby, Node.js, Elixir, Erlang & more
Visual Studio Code - Visual Studio Code
winget-cli - WinGet is the Windows Package Manager. This project includes a CLI (Command Line Interface), PowerShell modules, and a COM (Component Object Model) API (Application Programming Interface).
osxfuse - FUSE extends macOS by adding support for user space file systems
Chocolatey - Chocolatey - the package manager for Windows
Docker-OSX - Run macOS VM in a Docker! Run near native OSX-KVM in Docker! X11 Forwarding! CI/CD for OS X Security Research! Docker mac Containers.
ohmyzsh - 🙃 A delightful community-driven (with 2,200+ contributors) framework for managing your zsh configuration. Includes 300+ optional plugins (rails, git, macOS, hub, docker, homebrew, node, php, python, etc), 140+ themes to spice up your morning, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.
nvm - Node Version Manager - POSIX-compliant bash script to manage multiple active node.js versions
chromebrew - Package manager for Chrome OS [Moved to: https://github.com/chromebrew/chromebrew]
Scoop - A command-line installer for Windows.
PHP Brew - Brew & manage PHP versions in pure PHP at HOME