salmon

There are 2 repositories under salmon topic.

• COMBINE-lab / salmon

  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

  10xbioinformaticsc-plus-plusgene-expressionquantificationquasi-mappingrna-seqrna-seq-quantificationrnaseqsailfishsalmonscrna-seqselective-alignmentsingle-cellsingle-cell-rna-seqtranscriptome
  Language:C++ 829

• hyunhwan-jeong / SalmonTE

  SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

  pipelinengs-analysistransposable-elementssalmon
  Language:Jupyter Notebook 89

• mastodon / ostatus2

  A Ruby toolset for interacting with the OStatus suite of protocols

  salmonostatus
  Language:Ruby 31

• Novartis / pisces

  PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

  bioinformatics-pipelinernaseq-pipelinetranscriptomicssalmonbioinformaticsrnaseq
  Language:Python 29

• thelovelab / fishpond

  Differential expression and allelic analysis, nonparametric statistics

  rnaseqbioconductorstatisticsgenomicstranscriptomicsgene-expressionsalmonscrnaseq
  Language:R 28

• yyoshiaki / ikra

  RNAseq pipeline centered on Salmon

  salmonilluminaiongencodetranscript
  Language:Shell 27

• OStatus / spec

  OStatus Specification

  ostatusmicrobloggingfederated-social-webspecsalmonwebfinger
  Language:HTML 20

• Juke34 / AliNe

  Nextflow Alignment Pipeline - from fastq.gz to sorted bam with ease

  bowtie2bwahisat2minimap2nextflownucmerstargraphmap2bbmapbowtiekallistongmlrnovoalignsubreadbwa-swsublongbmw-mem2salmonstarlonglast
  Language:Nextflow 16

• pfefferle / wordpress-salmon

  A salmon plugin for WordPress

  wordpressostatuswordpress-pluginsalmonsalmon-protocolplugin
  Language:PHP 9

• iamcal / homespring.js

  A JavaScript interpreter for Homespring

  homespringinterpretersalmon
  Language:JavaScript 6

• nwfsc-cb / rCAX

  rCAX R package: an R client to access the REST API for the StreamNet Coordinated Assessments tables

  noaar-packagerest-apisalmon
  Language:R 5

• SoniaRuiz / coexp-website

  CoExp website is a web-based tool developed in .NET Core Framework, for querying 109 independent gene co-expression networks from the family of CoExp R packages.

  co-expressioncoexp-webpagegenetic-algorithmssalmoncsharphtml5html-css-javascriptjquerymvc-frameworkmvc-architecturenetcore3apachekestrel
  Language:JavaScript 5

• dapperstats / salvage

  Code for smooth interactions with the salvage database

  californiadeltacontinuous-deploymentsalvagesalmonsmelt
  Language:HTML 4

• asendia / salmonfit

  Frontend code of salmonfit.com

  ampsveltesalmonnetlifypwa
  Language:Svelte 3

• InfiniteTeam / SalmonBot

  연어봇 - SalmonBot

  discorddiscord-botdiscord-pydiscord-py-rewritepythonpython3salmon
  Language:Python 3

• mku11 / Salmon-Vault

  Secure all your personal files in Salmon Vault with AES-256 encryption for your Android, Windows, Linux, MacOS devices. Powered by Salmon AES CTR library.

  aes-256filejavavaultcsharpjavascriptmauixamarinsalmon
  Language:C# 3

• ORE-DiaPFC / Abondance

  Mise à jour et standardisation des séries chronologiques d'abondance du saumon atlantique sur les cours d'eau de l'ORE DiaPFC

  salmonabundance-estimationmodelingbayesian-inference
  Language:HTML 3

• sk7-dotcom / Evaluating_RNAseq_aligners

  Evaluating HISAT2, Salmon and Kallisto alignment using Checkpoint Blockade treated CT26 Experimental Data

  hisat2salmonkallistorna-seq
  Language:HTML 3

• bissessk / RNA-seq-Analysis-of-Control-and-NRDE2-depleted-Breast-Cancer-Cells

  Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.

  next-generation-sequencingngsngs-analysisrna-seqrnaseqrna-seq-analysisrna-seq-pipelinerna-seq-datarna-sequencingsalmonsalmon-deseq2tximportdeseq2rrstudiohpcunixlinuxbioinformaticsbioinformatics-pipeline
  Language:Shell 2
• SMG5-SMG7

  boehmv / SMG5-SMG7

  Code and scripts for the RNA-seq analysis of project: SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity

  alternative-splicingbioinformaticsdeseq2gencodeisoform-switchesleafcutternmdrrna-seqsalmon
  Language:R 2

• boehmv / UPF3

  Code and scripts for the RNA-seq analysis of project: Deciphering the cellular roles and dissecting functional regions of UPF3A and UPF3B in human NMD

  alternative-splicingbioinformaticsdeseq2gencodeisoform-switchesleafcutternmdrrna-seqsalmon
  Language:R 2

• danStich / dia

  An R package for the National Oceanic and Atmospheric Administration dam impact analysis

  damsr-packagesfishsalmondam-impact-analysissimulation
  Language:R 2

• KowalskiBio / RaptorQuant

  An easy pipeline to analyze data with Salmon.

  rnaseqrnaseq-pipelinesalmon
  Language:HTML 2

• mdscheuerell / AukeCoho

  Development site for an integrated population model for Auke Creek coho salmon

  rstanbayesian-data-analysissalmon
  Language:HTML 2

• nwfsc-math-bio / VRData

  Spawner and fraction wild data for the NWFSC Status Reviews.

  dataprotected-speciesr-packagesalmon
  Language:R 2

• srp33 / ExpressionAble

  Transform, query, and merge tabular files with the expressionable Python module. This tool is used primarily for gene-expression data.

  biologyrna-seqmicroarray-datahdf5gctarffparquetstatamsgpackpickletsvjsonfiltertranscriptiongene-expressionkallistosalmontabular-datamergetransforming-files
  Language:HTML 2

• srp33 / ExpressionAble-CLI

  Transform, query, and merge tabular files with the expressionable command-line tool. This tool is used primarily for gene-expression data.

  tsvgctarffparquetstatamsgpackhdf5pickletransforming-filesfiltertranscriptiongene-expressionkallistosalmontabular-datamerge
  Language:Python 2

• tdayris-perso / rna-dge-salmon-deseq2

  Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2

  snakemake-workflowsbioinformatics-pipelinereproducible-researchdeseq2salmontximportdifferential-expression
  Language:Python 2

• yejg2017 / Sequence-Mapping-Bio

  This is a code tutorial for rna or dna sequence mapping by myself-RyanYip

  fastqchtseqsalmonstarbowtie2featurecountsmultiqc
  Language:Shell 2

• fionacarson / salmon_density_dashboard

  Density of juvenile salmon in Caithness rivers - R-shiny dashboard

  dashboardrriverssalmoncaithness
  Language:R 1

• nwfsc-math-bio / NWCTrends

  This is an R package that runs the standardized trends metrics used in the 5-year Viability Reports for listed PNW salmonids.

  marssnoaar-packagesalmontime-seriesprotected-species
  Language:R 1

• Pinky-cloud224 / snakemake_workflow_rna_seq_data_analysis

  condaconfigcutadaptfastq-filesfastqcfeaturecountshtseq-countjupyter-notebookkallistomultiqcpaired-endpython3rna-seqsalmonsnakemake-workflowtpm
  Language:Jupyter Notebook 1

• salish-sea / orca-salmon

  A dashboard visualizing Chinook salmon returns to the Fraser and Columbia Rivers and Southern Resident killer whales occurrence

  ecosystemorcasalmon
  Language:Python 1

• salmon-forecasting / workshop-2024

  Information for a workshop on salmon forecasting sponsored by the USGS Cooperative Units Program. Participants include scientists from state and federal agencies in California, Oregon, Washington, and Idaho.

  forecastingsalmontime-series
  Language:HTML 1

• salmoncoast / Sea-lice-database

  Data from a longterm sea lice monitoring in the Broughton Archipelago, British Columbia, Canada by Alexandra Morton (Raincoast Research) and the Salmon Coast Field Station (salmoncoast.org)

  salmonsealiceecologyparasite
  Language:R 1

• tdayris-perso / rna-count-salmon

  Snakemake workflow for Salmon quantification and FastQC quality controls

  snakemake-workflowsbioinformatics-pipelinereproducible-workflowsrnaseq-pipelinefastqcsalmonmultiqc
  Language:Python 1