Salmon github. GitHub is where people build software.

Salmon github Add an optional note: Please don't include any personal information such as legal names or email addresses. Jul 2, 2025 · sake-salmon / design-tools Public Notifications You must be signed in to change notification settings Fork 0 Star 0 Requirements # Binary Releases # Pre-compiled binaries of the latest release of Salmon for a number different platforms are available available under the Releases tab of Salmon’s GitHub repository. wicked-fast) and while using little memory. Feb 11, 2020 · My current version of salmon is 0. Learn more about reporting abuse. Mar 11, 2023 · Salmon is a software package for quantifying transcriptomes from RNA-seq data. We moved from using the RapMap index to using a pufferfish based index. More recently, DFO’s State of the Salmon Program developed a streamlined approach to assess biological statuses of Pacific Salmon Conservation Units (CUs) through Wild Salmon Policy (WSP) rapid status assessments. e. - nf-core/rnaseq Alevin # Alevin is a tool — integrated with the salmon software — that introduces a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data. Now after typing in this script in the command line in my Terminal on my Mac, I get the follow smokin-salmon has one repository available. You can visit Salmon’s GitHub page here, and check out the Salmon source code, feature requests, known issues etc. 3-0, 1. avisalmon has 37 repositories available. Julia-salmon has one repository available. Mar 19, 2018 · I used salmon 0. Salmon Popular repositories web. Whether engaging in Object-Oriented Programming, utilizing First-Class Functions, or exploring the intracacies of dynamic typing, Salmon provides a frexible and powerful platform for software development. More than 150 million people use GitHub to discover, fork, and contribute to over 420 million projects. I have asked many QuantSeq related questions on this GH forum and I am yet to find the correct recipe Learn more about blocking users. Dec 28, 2024 · Tech-salmon has 6 repositories available. 14. salmon-1. 输入三文鱼密钥验证 salmon has 10 repositories available. Quantification of transcript abundance using Salmon View on GitHub Approximate time: 1. Currently alevin supports the following single-cell protocols: Drop-seq 10x-Chromium v1/2/3 inDropV2 CELSeq 1/2 Quartz-Seq2 sci-RNA-seq3 Alevin works under the same indexing scheme (as salmon) for the reference, and Alignment using Salmon Salmon Aligner Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. salmon -v salmon 0. 0) to quantify transcript abundance using full-length cDNA reads (ONT) after mapping with minimap2 to a transcriptome This repostory contatins the offical code both for evaluting your model using SALMon, and for generating SALMon data - as described in the paper "A Suite for Acoustic Language Model Evaluation" (ICASSP 2025 - Oral). "SALMON: Survival Analysis Learning with Multi-Omics Neural Networks on Breast Cancer. Requirements # Binary Releases # Pre-compiled binaries of the latest release of Salmon for a number different platforms are available available under the Releases tab of Salmon’s GitHub repository. Discuss code, ask questions & collaborate with the developer community. 0 forward), is a major feature enhancement introduced in recent versions of salmon. Q: What is salmon? A: salmon is a program for quickly and accurately estimating transcript-level abundance from RNA-seq data. A affordable and easy Minecraft server host! GitHub is where Salmon builds software. Optionally, Salmon can make use of pre-computed alignments (in the form of a Salmon is a wicked -fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. salmon uploading tools~. When salmon is run with selective alignment, it adopts a considerably more sensitive scheme that we have developed for finding the potential mapping loci Contribute to SalmonDXH/Anime-Vanguard-AIO-Macro development by creating an account on GitHub. 1 successfully a few weeks ago. If you think you have a common question, let us know, and we’ll consider adding it to this page. [Link] The generation of the reduced alignment data (RAD) files processed by alevin-fry is done by either piscem or salmon. At salmon v1. 0a0 depends icu: depends libcurl: >=8. License: GPLv3 Home: https://github. Salmon has 4 repositories available. Contribute to KyokoMiki/smoked-salmon-windows development by creating an account on GitHub. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects. 0, I'v tried the command "conda update salmon" but the version remains 0. Oct 29, 2020 · Thanks @rob-p and Thanks in advance @mikelove The original question pertained to using salmon with say ILMN RNA-Seq followed by DGE with DESeq2 @rob-p - I will also use this opportunity to indulge myself on a related question (how to use salmon with QuantSeq and then downstream with DESeq2). Salmon performs its inference using an expressive and Oxford Nanopore Technologies (ONT) long read quantification Author: Hossein Asghari, Computational Biologist at Ocean Genomics This project has been made possible by the team at Ocean Genomics, and by a grant from the Chan Zuckerberg Initiative. 1. Learn more about blocking users. Salmon The Pacific Salmon Foundation ’s Salmon Watersheds Program is working to help foster healthy, diverse and abundant wild salmon populations throughout British Columbia. Quick start usage instructions can be found on the Wiki Usage page. dev Public Forked from desenmeng/web. Jul 4, 2025 · Contribute to SalmonDXH/Anime-Vanguard-AIO-Macro development by creating an account on GitHub. Sep 22, 2022 · Hi salmon team, Thank you for developing this useful tool! I used salmon (v1. 1038/nmeth. GitHub is where people build software. Contribute to moggers87/salmon development by creating an account on GitHub. Aug 3, 2021 · Hi @rudondamba, Thanks for the report. 3-2, 1. Salmon achieves its accuracy and speed via a number of different innovations, including the use of selective-alignment (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference Dec 13, 2018 · I'm planning on using your wonderful Salmon tool v0. Q: What is mapping validation COMputational BIology and Network Evolution lab. Contribute to sake-salmon/design-tools development by creating an account on GitHub. Prevent this user from interacting with your repositories and sending you notifications. If STAR is run with the --quantMode TranscriptomeSAM flag (and without sorting the output BAM file), it should work as is. The simpleaf repository contains a dedicated wrapper / workflow runner for processing data with alevin-fry that vastly simplifies both the creation of extended references and the subsequent quantification of Alevin is a tool --- integrated with the salmon software --- that introduces a family of algorithms for quantification and analysis of 3' tagged-end single-cell sequencing data. ksalmon has 26 repositories available. In this lesson we walk through the The current enumeration strategy is to use one computer vision model to detect and recognize the salmon species and then run a multi-object tracking algorithm such as ByteTrack or BoT-SORT to track the salmon and count it. 9. Now, I am Contribute to SalmonDXH/Anime-Vanguard-AIO-Macro development by creating an account on GitHub. 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment - COMBINE-lab/salmon Nov 25, 2021 · Expression quantification with salmon. With a SALMON-TDDFT has 6 repositories available. 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment - COMBINE-lab/salmon Quantification of transcript abundance using Salmon View on GitHub Approximate time: 30 minutes Learning Objectives Create a job submission script to run Salmon on all samples in the dataset Running Salmon on multiple samples In class we talked in depth about how the Salmon algorithm works, and provided the command required to run Salmon on a single sample. R(esearch) Software Engineer, Blogger. It is developed openly on GitHub. Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Contribute to Salmon-B0T/SalmonHub development by creating an account on GitHub. github. 3-4, 1. Follow their code on GitHub. We would like to show you a description here but the site won’t allow us. There are more details about this in about page. This means that, you'll want to rebuild your index using a recent version of salmon. Any idea how STAR was run here? Presumably you can get the command line from Aug 3, 2022 · Conda See the ‘activating the conda environment’ section below to access this software. Repositories Salmon Public The Salmon Programming Language, a dynamically typed, garbage collected, general purpose language C 2 MIT 1 1 (1 issue needs help) 0 Updated on Jan 23, 2024 Salmon-lang. " Frontiers in Genetics 10 (2019): 166. Contribute to SALMON-TDDFT/SALMON2 development by creating an account on GitHub. 8,<2. The result is Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (an accurate but fast-to-compute proxy for traditional read alignments) a two-phase inference procedure that makes use of massively-parallel stochastic collapsed Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. Optionally, Salmon can make use of pre-computed alignments (in the Links: biotools: salmon, usegalaxy-eu: salmon, usegalaxy-eu: salmonquantmerge, usegalaxy-eu: alevin, doi: 10. SalmonDXH has 13 repositories available. Explore the GitHub Discussions forum for COMBINE-lab salmon. Mar 3, 2025 · 🚀🚀 Welcome to the repo of SALMONN! The SALMONN model family consists of a series of advanced multi-modal large language models. Mar 11, 2023 · 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment - COMBINE-lab/salmon GitHub is where people build software. Aug 25, 2021 · GitHub is where people build software. 12. Currently alevin supports the following single-cell protocols: Drop-seq 10x-Chromium v1/2/3 inDropV2 CELSeq 1/2 Quartz-Seq2 sci-RNA-seq3 Alevin works under the same indexing scheme (as salmon) for the Dec 19, 2018 · SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances from Next Generation Sequencing Data. Contribute to COMBINE-lab/SalmonTools development by creating an account on GitHub. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i. Mar 15, 2023 · Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)? Salmon index Describe the bug Hi, I have tried a big reference file before and It was succesfully created. Q: What is mapping validation smoked-salmon runs in CLI mode, except for spectral visualization, which launches a web server. More than 94 million people use GitHub to discover, fork, and contribute to over 330 million projects. Assuming a conda environment is already set up, we can install salmon through following command: What is Salmon? Salmon is a wicked -fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. COMBINE lab has 128 repositories available. Contact GitHub support about this user’s behavior. 0a0 depends designweb. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. com/COMBINE-lab/salmon 499978 total downloads Last upload: 5 months and 22 days ago This page hosts a (potentially growing) list of frequently-asked questions about salmon. It uses new algorithms and a realistic model of RNA-seq data to provide accurate and quick results. This page hosts a (potentially growing) list of frequently-asked questions about salmon. This note will be visible to only you. i make thing. Installing Salmon Although there are mutliple ways to download salmon (ex: binary from github, docker image), we are going to install it through conda. 4197 package salmon ¶ versions: 1. not providing whitelist, forceCells 3000 [20 Salmon ¶ Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. Salmon-B0T has 4 repositories available. You can read the details of the pipeline and an example of real data study in my recent published paper in PSB 2018. Salmon515 has 3 repositories available. 5 days ago · This tool converts Salmon V1 configuration files into Salmon V2–compatible configs. Feb 22, 2023 · Description of the bug Hi, I have been having issues with nf-core/rnaseq erroring out at the salmon step. All you need to run Salmon is a FASTA file containing your reference transcripts and a (set of) FASTA/FASTQ file (s) containing your reads. dev The frontend, backend, and content source code for web. io Public The website for salmon 0 Apache-2. Roblox Anime Vanguard Macro by Salmon. jjslmn has 5 repositories available. Salmon is a wicked -fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Optionally, Salmon can make use of pre-computed alignments (in the SALMON is a new RLAIF paradigm for self-aligning language models from scratch, using only a small set of human-defined principles as guidance. 1-2, 1. Useful tools for working with Salmon output. 0,<9. 0, there was a breaking change in the index used in salmon. dev JavaScript sake-salmon has 3 repositories available. 0 Try out the new alevin-fry framework for single-cell analysis; tutorials can be found here! Help guide the development of Salmon, take our survey What is Salmon? Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. 0. We use YOLOv8 that provides a suite of tools to perform these two tasks simultaneously during the inferencing step. 0 when not providing whitelist the mapping rate is low 20%, and many reads are discarded because of the noisy barcodes. After quantification Obtaining Salmon Salmon is a free (both as in “free beer” and “free speech”) software tool for estimating transcript-level abundance from RNA-seq read data. Moved to Codeberg. The Salmon Watersheds Program works to strengthen the baseline of scientific information available for wild Pacific salmon populations and their habitats. I am using the latest update according to miniconda. Central to our approach is a principle-following reward model. For more details, please refer to the corresponding branches Note Selective alignment Selective alignment, first introduced by the --validateMappings flag in salmon, and now the default mapping strategy (in version 1. Huang, Zhi, et al. Trained on synthetic preference data, this model can generate reward scores based on arbitrary human-defined principles. 3-3, 1. It supports both Strategy and Coordinate conversion with a simple graphical interface. Sep 13, 2024 · GitHub is where people build software. We strive to make this information broadly accessible to federal RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. 0 Development Repository. maelle has 317 repositories available. 3-1, 1. Maximum 100 characters, markdown supported. GitHub Gist: instantly share code, notes, and snippets. The result is Note Selective alignment Selective alignment, first introduced by the --validateMappings flag in salmon, and now the default mapping strategy (in version 1. 3-5, 1. script thing. 13. The result is a versatile tool that fits nicely into many different pipelines. Salmon achieves its accuracy and speed via a number of different innovations, including the use of selective-alignment (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. Salmon ¶ Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. You should be able to get started quickly by finding a binary from the list that is compatible with your platform. Browse the latest releases of Salmon on GitHub, with features, fixes, improvements and changelogs. 25 hours Learning Objectives Use lightweight algorithms to quantify reads to abundance estimates Explain how Salmon performs quasi-mapping and transcript abundance estimation Lightweight alignment and quantification of gene expression Now that we have explored the quality of our raw reads, we can move on to Salmon offers a versitile and expressive programming environment, facilitating a wide range of programming paradimes. 2-0, 1. Contribute to SalmonDXH/Anime-Vanguard-AIO-Macro development by creating an account on GitHub. Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. When salmon is run with selective alignment, it adopts a considerably more sensitive scheme that we have developed for finding the potential mapping loci After quantification Obtaining Salmon Salmon is a free (both as in “free beer” and “free speech”) software tool for estimating transcript-level abundance from RNA-seq read data. 0 for generating TPM counts with a view to quantifying relative abundance of certain bacterial antibiotic resistance genes in my shotgun (huma Mar 11, 2023 · 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment - COMBINE-lab/salmon. 0 0 0 0 Updated on Jan 8, 2024 We would like to show you a description here but the site won’t allow us. Salmon Using Salmon Preparing transcriptome indices (mapping-based mode) Quantifying in mapping-based mode Quantifying in alignment-based mode Description of some important options What’s this LIBTYPE? Output Misc References Alevin Using Alevin Providing multiple read files to Alevin Description of important options Single-cell protocol Salmon achieves its accuracy and speed via a number of different innovations, including the use of selective-alignment (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. This repository has teaching materials for a 3-day Introduction to bulk RNA-seq: From reads to count matrix workshop. It comes with Salmon which is a fast and accurate transcriptome quantification method. 1 and I need to upgrade to version 1. SALMON 2. Further, the move to the pufferfish index drops support for the FMD-like index, so you can remove the --type argument. 1-1, depends boost-cpp: depends bzip2: >=1. The latest version of both are available on GitHub and via bioconda. Nov 4, 2020 · The assumptions made by salmon regarding the BAM files are the same as those made by RSEM (with the exception that salmon will accept alignments with insertions or deletions in the CIGAR strings). 10. This workshop focuses on teaching basic computational skills to enable the effective use of an high-performance computing environment to implement an RNA-seq data analysis workflow Jan 29, 2019 · Hi, I am using Alevin to process some 10x v2 data. Contribute to momo881/av-macro development by creating an account on GitHub. I've got a lengthy discussion over at the salmon github page Sr Staff Software Engineer @ Simbe Robotics. vfojz zofjuz zuefxwp rlodc ilqqy uvsv ackcg hxvqntl lrppdq pxyrkoq ffaq hmlotc yhatb dlx akjt