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149 search results found
Papermill
⭐
5,513
📚 Parameterize, execute, and analyze notebooks
Drake
⭐
1,332
An R-focused pipeline toolkit for reproducibility and high-performance computing
Targets
⭐
860
Function-oriented Make-like declarative workflows for R
Corrr
⭐
580
Explore correlations in R
Scrna Seq_notes
⭐
478
A list of scRNA-seq analysis tools
Zumis
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232
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
Snapatac
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227
Analysis Pipeline for Single Cell ATAC-seq
Piper
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151
Multi-Paradigm Pipeline Implementation
Rnaseq Workflow
⭐
133
A repository for setting up a RNAseq workflow
Mlr3pipelines
⭐
127
Dataflow Programming for Machine Learning in R
Gwas_scripts
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127
Codebook from my GWAS cookbook
Tarchetypes
⭐
108
Archetypes for targets and pipelines
Cargo Deny Action
⭐
100
❌ GitHub Action for cargo-deny 🦀
Targets Tutorial
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90
Short course on the targets R package
Intubate
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73
<||> Interfaces to Popular R Functions for Data Science Pipelines, and More
Opencyto
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71
A package that provides data analysis pipeline for flow cytometry.
Scatac Pro
⭐
64
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Pipeliner
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61
Machine learning pipelines for R.
Targets Shiny
⭐
60
Example Shiny app containing a targets pipeline.
Irap
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58
integrated RNA-seq Analysis Pipeline
Drake Examples
⭐
58
Example workflows for the drake R package
Meteore
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58
Automatic DNA methylation detection from nanopore tools and their consensus model
Drake
⭐
57
The user manual for the drake R package
Nozzle
⭐
55
Nozzle is a report generation toolkit for data analysis pipelines implemented in R.
Rmonad
⭐
54
Pipelines you can compute on
Tenx
⭐
53
Pipelines for the analysis of 10x single-cell RNA-sequencing data
Tomicsvis
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50
Transcriptomics Visualization R package.
Pepatac
⭐
48
A modular, containerized pipeline for ATAC-seq data processing
Mikropml
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48
User-Friendly R Package for Supervised Machine Learning Pipelines
Tamper
⭐
47
Easier debugging of magrittr pipes
Firebrowser
⭐
47
An R client for broads firehose pipeline, providing TCGA data sets
Targets Minimal
⭐
45
A minimal example data analysis project with the targets R package
Cytofkit
⭐
42
cytofkit: an integrated flow/mass cytometry data analysis pipeline
Sparkxgb
⭐
40
R interface for XGBoost on Spark
Get_phylomarkers
⭐
39
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Needlestack
⭐
39
Multi-sample somatic variant caller
Rqdatatable
⭐
38
Implement the rquery piped query algebra in R using data.table. Distributed under choice of GPL-2 or GPL-3 license.
Pipecleaner
⭐
37
Debug and Refactor magrittr Pipelines
Qtlmap
⭐
36
Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
Samsa2
⭐
35
SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
Hes_pipeline
⭐
33
R pipeline to clean and process Hospital Episode Statistics (HES) data
Ruigi
⭐
33
Ruigi is a pipeline specialist, much like his python counterpart, Luigi.
Pipecomp
⭐
31
A R framework for pipeline benchmarking, with application to single-cell RNAseq
Ltrpred
⭐
31
De novo annotation of young retrotransposons
Simplecache
⭐
30
Simplified R caching for reproducible big data projects
Tdastats
⭐
28
R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.
Rap_companion
⭐
27
A technical communication document intended to give assistance to people developing a Reproducible Analytical Pipeline.
Make Activity
⭐
26
Walks through the hands-on activity showing how to automate a data analytical pipeline with make
Computer Architecture Task 2
⭐
25
Riscv32 CPU Project
Sigflow
⭐
25
Sigflow: Streamline Analysis Workflows for Mutational Signatures
Madr_pipelines
⭐
25
Slides and materials for my talk to the Madison R Users Group
Jamp
⭐
24
JAMP - Just Another Metabarcoding Pipeline
Makepipe
⭐
24
Tools for constructing simple make-like pipelines in R.
Phylotar
⭐
24
An automated pipeline for retrieving orthologous DNA sequences from GenBank in R
Pharmacogenomics_prediction_pipeline_p3
⭐
23
Mleap
⭐
23
R Interface to MLeap
Gnomad Sv Pipeline
⭐
22
Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
Rmlops
⭐
22
MLOps with R and Azure Pipelines
R Azure Pipelines
⭐
22
Test package for azure pipelines
Rtpc
⭐
21
R package to help fit Thermal Performance Curves
Limma Pipeline Proteomics
⭐
21
LIMMA (an empirical Bayes method) pipeline for two group comparison in a proteomic experiment
Nflwar
⭐
20
An R package to compute WAR for offensive players using nflscrapR
Wg Blimp
⭐
20
wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data
Analysis Pipelines
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20
Enables data scientists to compose pipelines of analysis which consist of data manipulation, exploratory analysis & reporting, as well as modeling steps. Data scientists can use tools of their choice through an R interface, and compose interoperable pipelines between R, Spark, and Python.
Rna Seq Snakemake
⭐
20
Snakemake based pipeline for RNA-Seq analysis
Mageckflute
⭐
20
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Ngspipe2go
⭐
19
a set of NGS pipelines
Smurf
⭐
19
Dimsum
⭐
18
An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies
Exorthist
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18
ExOrthist: a pipeline to extract exon orthologies at any evolutionary distance.
Stackr
⭐
17
stackr: an R package to run stacks software pipeline
Pipe4c
⭐
17
4C-seq processing pipeline
Handwriter
⭐
17
Forensic Handwriting Analysis Pipeline in R - Please download our stable version from CRAN using 'install.packages("handwriter")'
Network_snps
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17
A framework for network analysis and display of SNPs
Blood_rnaseq_rare_disease_paper
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17
Targets
⭐
16
User manual of the targets R pacakge
Sincera
⭐
16
An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis
Calculating Fusion Twas Weights Pipeline
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15
This is a pipeline for calculating weights for TWAS
Exprso
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15
An R package to rapidly build and deploy supervised machine learning workflows
Data Factory R Server Apache Spark Pipeline
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15
This tutorial highlights how to build a scalable machine-learning based data processing pipeline using Microsoft R Server with Apache Spark utilizing Azure Data Factory (ADF)
Parser
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15
parseR: Pipeline for rna-seq analysis in R
Hrdetect Pipeline
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15
Targetsketch
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15
Sketch a pipeline of targets in an interactive web app
Gwena
⭐
15
Gene Co-expression Network analysis pipeline
Pipecomposer
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14
Metax
⭐
14
metaX: a flexible and comprehensive software for processing omics data.
Rnaseq
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13
RNA-seq, QC and differential analysis pipeline
Post Gwas Pipeline
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12
A comprehensive pipeline for post-GWAS analysis leveraging diverse types of omics data
Psap Pipeline
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12
Ontrack
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12
A MinION-based pipeline for tracking species biodiversity
Introduction_to_gwas
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11
https://filippob.github.io/introduction_to_gwas/
Mandrake
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11
📖🐉- Bring reading the manual 📖 closer to your drake 🐉 workflow 🔥
Validata
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11
validates data imports in analysis pipeline
Targets Stan
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11
An example project to validate a Stan model in a targets pipeline
Catd_snakemake
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11
Snakemake pipeline for benchmarking cell-type deconvolution methods as well as deconvoluting real bulk RNA-seq data with the use of scRNA-seq datasets
Soccer Analytics With Python Mongodb And R
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11
using python, NoSQL(mongoDB), elastic search, kibana, marvel & R for pipeline structure
Condusco
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11
query-driven query generation in R
Sppider
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10
a tool to identify species and inter-species hybrids and chromosome copy number variants from short-read data
Cancer Biomarker Prediction Pipeline Campp
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10
The Cancer bioMarker Prediction Pipeline (CAMPP)
Neon Is Data Processing
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10
Next generation data processing algorithms and pipeline components for (most) NEON TIS and AIS data products.
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