Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: salmon
danStich/dia
An R package for hosting data & code, and for running the Dam Impact Analysis (DIA) developed by Nieland et al. (2015)
Language: CSS - Size: 923 KB - Last synced: 4 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
Novartis/pisces
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
Language: Python - Size: 17.6 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 28 - Forks: 3
pfefferle/wordpress-salmon π¦
A salmon plugin for WordPress
Language: PHP - Size: 136 KB - Last synced: 15 days ago - Pushed: about 4 years ago - Stars: 9 - Forks: 5
NickCrews/SmartSeiner π¦
Data-driven salmon fishing
Language: Jupyter Notebook - Size: 27.7 MB - Last synced: 22 days ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0
ORE-DiaPFC/Abondance
Mise Γ jour et standardisation des sΓ©ries chronologiques d'abondance du saumon atlantique sur les cours d'eau de l'ORE DiaPFC
Language: HTML - Size: 98.5 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 2 - Forks: 0
USFWS/escapement
https://usfws.github.io/escapement/
Language: HTML - Size: 3.59 MB - Last synced: 30 days ago - Pushed: 12 months ago - Stars: 0 - Forks: 0
dapperstats/salvage
Code for smooth interactions with the salvage database
Language: HTML - Size: 223 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 4 - Forks: 0
COMBINE-lab/salmon
π π£ π± Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Language: C++ - Size: 209 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 725 - Forks: 156
thelovelab/fishpond
Differential expression and allelic analysis, nonparametric statistics
Language: R - Size: 7.01 MB - Last synced: 8 days ago - Pushed: 9 months ago - Stars: 24 - Forks: 9
noaa-nwfsc/pycax
Python client for the CAX API. Holmes, E. E and M. Williams. 2023. pycax: a Python client for the Coordinated Assessments data exchange REST API
Language: Jupyter Notebook - Size: 5.96 MB - Last synced: 12 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
michalbukowski/dge-ontology
Jupyter notebooks for DGE results and ontology analysis and visualisation.
Language: Jupyter Notebook - Size: 1.09 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0
julianneyang/transcriptomicsonhoffman
Walks through installation and usage of FASTQC, MultiQC, Trimmomatic, and Salmon for transcriptomic data preprocessing. Includes Grid Engine shell scripts that can be looped over many files in a directory.
Language: R - Size: 20.9 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0
argon11110/Lakseteller
Salmon Time
Language: Python - Size: 1.95 KB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
noaa-nwfsc/VRAPCpp
R package for VRAP rewrite
Language: R - Size: 10.9 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
michalbukowski/rnaseq-pipeline-2
Simple Nextflow RNA-Seq pipeline
Language: Nextflow - Size: 871 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
SherineAwad/BulkRNASeq
Snakemake workflow for Bulk RNASeq at both genome level and transcripts level.
Language: R - Size: 94.7 KB - Last synced: 4 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0
GalaxyPickle/Sammy_the_Salmon
A 3D game about being a salmon who makes the incredible journey from the ocean back up to his spawning grounds.
Language: C# - Size: 121 MB - Last synced: 4 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1
nwfsc-cb/rCAX
rCAX R package: an R client to access the REST API for the StreamNet Coordinated Assessments tables
Language: R - Size: 1.74 MB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 5 - Forks: 1
mastodon/ostatus2 π¦
A Ruby toolset for interacting with the OStatus suite of protocols
Language: Ruby - Size: 30.3 KB - Last synced: 16 days ago - Pushed: over 4 years ago - Stars: 32 - Forks: 9
zeroware/ostatus π¦
A JavaScript toolset for interacting with the OStatus suite of protocols (JS port of tootsuite/ostatus2)
Language: JavaScript - Size: 14.6 KB - Last synced: about 1 month ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0
salish-sea/orca-salmon Fork of liu-zoe/orcasalmon
A dashboard visualizing Chinook salmon returns to the Fraser and Columbia Rivers and Southern Resident killer whales occurrence
Language: Python - Size: 15.5 MB - Last synced: 5 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0
ADFG-DSF/DeshkaWeir
Deshka Weir Chinook and Coho ASL
Language: HTML - Size: 4.69 MB - Last synced: 4 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0
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.
Language: JavaScript - Size: 51.6 MB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 6 - Forks: 1
sk7-dotcom/Evaluating_RNAseq_aligners
Evaluating HISAT2, Salmon and Kallisto alignment using Checkpoint Blockade treated CT26 Experimental Data
Language: HTML - Size: 26.5 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0
tdayris-perso/rna-dge-salmon-deseq2 π¦
Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2
Language: Python - Size: 3.15 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 2
curryc2/Bristol-Bay-Run-Recon
A general run reconstruction model for the commercial sockeye salmon fishery in Bristol Bay, Alaska. This model leverages information from age and genetic composition samples to apportion mixed-stock catches and account for interception among terminal fishing districts.
Language: HTML - Size: 60.5 MB - Last synced: 2 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 2
hyunhwan-jeong/SalmonTE
SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
Language: Jupyter Notebook - Size: 258 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 75 - Forks: 22
PDXPCs/PDXPCs.github.io
A simple site about dams.
Language: HTML - Size: 8.34 MB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0
oxpeter/goncalo2019
Language: Jupyter Notebook - Size: 18.5 MB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0
yash199/MultiQC-Salmon
Adding Salmon-based Modules to MultiQC
Size: 35.2 KB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
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
Language: R - Size: 5.29 MB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0
eveskew/frog_chytrid_transcriptomics
Code, data, and figures for an experimental pathogen exposure study using wood frogs and American bullfrogs
Language: R - Size: 129 MB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
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.
Language: R - Size: 23.6 MB - Last synced: 10 months ago - Pushed: 12 months ago - Stars: 1 - Forks: 0
yyoshiaki/ikra
RNAseq pipeline centered on Salmon
Language: Shell - Size: 12 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 24 - Forks: 19
ADFG-DSF/Ricker_mean
Some information about whether the log-normal correction should be used in escapement goal analysis.
Language: R - Size: 493 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0
ADFG-DSF/UCI_EEZ
Fulfills a data request to estimate sport fish harvest in the Upper Cook Inlet Exclusive Economic Zone.
Language: HTML - Size: 9.5 MB - Last synced: 4 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0
mdscheuerell/AukeCoho
Development site for an integrated population model for Auke Creek coho salmon
Language: HTML - Size: 17.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0
InfiniteTeam/SalmonBot π¦
μ°μ΄λ΄ - SalmonBot
Language: Python - Size: 578 KB - Last synced: 19 days ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 6
asendia/salmonfit
Frontend code of salmonfit.com
Language: Svelte - Size: 17.6 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 3 - Forks: 0
nwfsc-math-bio/VRData
Spawner and fraction wild data for the NWFSC Status Reviews.
Language: R - Size: 50.4 MB - Last synced: 10 months ago - Pushed: about 2 years ago - Stars: 2 - Forks: 1
nwfsc-math-bio/VRReport
Sandbox project
Language: TeX - Size: 38.7 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
nwfsc-math-bio/DMVRAPapp
DMVRAP shiny application
Language: R - Size: 51.8 KB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
nwfsc-math-bio/DM
Dynamic Model
Language: R - Size: 166 KB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
nwfsc-math-bio/VRAP
R package for the VRAP program
Language: R - Size: 1.65 MB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0
jarleven/Salmon
Project to detect and classify fish in a river
Language: Jupyter Notebook - Size: 2.68 GB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1
Pinky-cloud224/snakemake_workflow_rna_seq_data_analysis
Language: Jupyter Notebook - Size: 975 KB - Last synced: 5 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
michalbukowski/rnaseq-pipeline-1
Simple Snakemake RNA-Seq pipeline
Language: Python - Size: 942 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
salmon-protocol/wordpress-salmon Fork of pfefferle/wordpress-salmon π¦
A salmon plugin for WordPress
Language: PHP - Size: 126 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0
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
Language: R - Size: 2.98 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 0
fionacarson/salmon_density_dashboard
Density of juvenile salmon in Caithness rivers - R-shiny dashboard
Language: R - Size: 1000 KB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
tdayris-perso/rna-count-salmon π¦
Snakemake workflow for Salmon quantification and FastQC quality controls
Language: Python - Size: 396 KB - Last synced: 4 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0
iamcal/homespring.js
A JavaScript interpreter for Homespring
Language: JavaScript - Size: 437 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0
atigano/kokanee_sockeye_WGR
Scripts accompanying manuscript "The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid"
Language: R - Size: 57.6 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
salmoncoast/Sea-lice-database Fork of sjpeacock/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)
Language: R - Size: 23.4 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 1
mikelove/Bioc2022AllelicExpression
Bioc2022 workshop. SEESAW: Statistical Estimation Of Allelic Expression Using Salmon And Swish
Language: R - Size: 46.1 MB - Last synced: 7 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1
OStatus/spec
OStatus Specification
Language: HTML - Size: 109 KB - Last synced: about 1 year ago - Pushed: about 9 years ago - Stars: 18 - Forks: 0
jianhong/genomictools
docker file for genomic tools
Language: Dockerfile - Size: 176 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 0
srp33/ExpressionAble-CLI
Transform, query, and merge tabular files with the expressionable command-line tool. This tool is used primarily for gene-expression data.
Language: Python - Size: 52.7 KB - Last synced: 5 days ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 0
gusg21/distributed-project
an unfinished game I worked on for my Distributed Computing class in high school
Language: C# - Size: 2.87 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0
isugifNF/RNAseq
RNAseq from fastq reads to gene counts/quantification
Language: Nextflow - Size: 994 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0
PSC-CoTC/PSC-FRAM-Admin
Administration tools and utilities used by the PSC Coho Technical Committee to administer FRAM model runs.
Language: HTML - Size: 969 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 1 - Forks: 1
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.
Language: Shell - Size: 418 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0
gustaveroussy/rna-count-salmon
Count your fastq-formatted rna-seq reads with Salmon
Language: Python - Size: 335 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1
ORE-DiaPFC/CIEM
Tables for the ICES Working Group on North Atlantic Salmon (WGNAS) for the ORE-DiaPFC rivers
Size: 29.3 KB - Last synced: 5 months ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 1
srp33/ExpressionAble
Transform, query, and merge tabular files with the expressionable Python module. This tool is used primarily for gene-expression data.
Language: HTML - Size: 12.4 MB - Last synced: 9 days ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 5
jimtyhurst/salmonstats
Functions to explore, analyze, and visualize open data about salmon.
Language: R - Size: 1.31 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1
jimtyhurst/statusAndTrends Fork of int-salmon-data-lab/statusAndTrends
Datasets and related knowledge from the International Year of the Salmon (IYS) "Salmon Status and Trends" workshops
Language: R - Size: 1.09 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0
martijnarts/homespring-js
AKA HOtMEfSPRIbNG
Language: JavaScript - Size: 23.4 KB - Last synced: 19 days ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0
megaptera-helvetiae/SalmoTruttaVals
Analysis of Salmo trutta gametes and embryo microbiome project in Vals/Trun, Switzerland
Language: R - Size: 1.23 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0
