noriakis/ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

Language: R - Size: 14.7 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 198 - Forks: 16

noriakis/metagenome-pipeline

Language: Ruby - Size: 69.3 KB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

noriakis/q2-pathway

QIIME 2 plugin for visualizing and analyzing pathway information based on gene family abundances

Language: Python - Size: 158 KB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

noriakis/scstruc

Gene regulatory network based on Bayesian network structure in single-cell transcriptomics

Language: R - Size: 4 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

noriakis/CBNplot

Bayesian network plot for the enrichment analysis results

Language: R - Size: 1.59 MB - Last synced: 16 days ago - Pushed: about 2 months ago - Stars: 52 - Forks: 11

noriakis/software

Size: 722 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 0

noriakis/pykegg

Analyze and visualize KEGG information using network approach

Language: Python - Size: 4.17 MB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 2 - Forks: 1

noriakis/stana

Metagenotyping analysis in R

Language: R - Size: 5.64 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 4 - Forks: 0

noriakis/biotextgraph

R library to make a summarized visualization of textual information by network

Language: R - Size: 6.16 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 7 - Forks: 1

noriakis/piphir

Functional prediction from 16S rRNA gene sequencing data using Piphillin algorithm in R

Language: R - Size: 42 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

noriakis/pubmedMini

Storing PMC article information for each gene query

Language: R - Size: 7.97 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

noriakis/edgebundle Fork of schochastics/edgebundle

R package implementing edge bundling algorithms

Language: R - Size: 11.1 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

noriakis/ccdrAlgorithm Fork of itsrainingdata/ccdrAlgorithm

Structure learning for Bayesian networks using the CCDr algorithm.

Language: C++ - Size: 322 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

noriakis/clusterlayouts

Network layouts using the cluster information

Language: R - Size: 4.06 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

noriakis/ggsc Fork of YuLab-SMU/ggsc

Size: 106 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

noriakis/misc

Miscellaneous data for the package

Size: 30.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

noriakis/MIDAS2_scripts

Scripts for MIDAS2 (Metagenomic Intra-Species Diversity Analysis System 2)

Language: Python - Size: 29.3 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

noriakis/tidySummarizedExperiment Fork of stemangiola/tidySummarizedExperiment

Brings SummarizedExperiment to tidiverse with no side-effects

Size: 949 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

noriakis/tidybn

Tidy manipulation of Bayesian network

Language: R - Size: 1.11 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

noriakis/tidySingleCellExperiment Fork of stemangiola/tidySingleCellExperiment

Brings SingleCellExperiment objects to the tidyverse

Size: 6.06 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

noriakis/tidygraph Fork of thomasp85/tidygraph

A tidy API for graph manipulation

Language: R - Size: 827 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

noriakis/tidyseurat Fork of stemangiola/tidyseurat

Seurat meets tidyverse. The best of both worlds.

Language: R - Size: 26.8 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

noriakis/gget Fork of pachterlab/gget

🧬 gget enables efficient querying of genomic reference databases

Language: Python - Size: 199 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

noriakis/MIDAS2NV Fork of czbiohub-sf/MIDAS2

Metagenomic Intra-Species Diversity Analysis 2 using GPU

Language: Python - Size: 196 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

noriakis/nvbio Fork of NVlabs/nvbio

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.

Language: C++ - Size: 6.51 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

noriakis/ckegg

Command line tool to examine KEGG PATHWAY

Language: C - Size: 20.5 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

noriakis/ggraph Fork of thomasp85/ggraph

Grammar of Graph Graphics

Language: R - Size: 2.54 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

noriakis/seqtk Fork of lh3/seqtk

Toolkit for processing sequences in FASTA/Q formats

Language: C - Size: 267 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

noriakis/pykegg-docs

Size: 5.66 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

noriakis/graphhighlight

highlight nodes and edges of ggraph plot

Language: R - Size: 558 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

noriakis/1dcnn-scorecam

Application of score-weighted class activation mapping on one dimensional CNN

Language: Jupyter Notebook - Size: 354 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

noriakis/BioCyjs

Size: 0 Bytes - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

noriakis/cpbnplot

Bayesian network plot for the enrichment analysis results

Language: Jupyter Notebook - Size: 1.33 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

noriakis/cyjs_test

testing the Cytoscape.js

Language: JavaScript - Size: 47 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

noriakis/MIDAS Fork of snayfach/MIDAS

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

Language: Python - Size: 106 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

noriakis/ggmidas

Import and plot output of MIDAS

Language: R - Size: 24.4 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

noriakis/metagenome_pipeline

Snakemake metagenome pipline

Language: Python - Size: 1000 Bytes - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

noriakis/CBNplotTest

Language: R - Size: 271 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

noriakis/OSplot

OSplot: easy visualization and interpretation of omics summary data

Size: 1000 Bytes - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

noriakis/shinsengumi

Shinsengumi-inspired color palettes for R

Language: R - Size: 2.93 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

noriakis/cvopt

Populate CheckV results

Language: Rust - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

noriakis/Cyjs-biological-pathway

Visualizing gene regulatory networks with pathway information by Cytoscape.js

Size: 0 Bytes - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

noriakis/textORA

over representation analysis for the gene description

Language: R - Size: 2.93 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

noriakis/cam-uncertainty

Language: Jupyter Notebook - Size: 78 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

noriakis/compare_sign

Language: R - Size: 906 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

noriakis/bootReason

Bootstrap probabilistic reasoning of Bayesian network

Language: R - Size: 2.93 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

noriakis/cplotnet

Size: 0 Bytes - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

noriakis/blog

Language: HTML - Size: 17.8 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

noriakis/sjrdataPlot

Inspect SJR data by Shiny application

Size: 233 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

noriakis/glomerulus-clustering

Size: 1.39 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

noriakis/adaptive-importance-sampling-BN Fork of kgourgou/adaptive-importance-sampling-BN

Experimental code: adaptive importance sampling for bayesian networks. -- I think I may have broken this code.

Size: 39.1 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

noriakis/ANCOM Fork of FrederickHuangLin/ANCOM-Code-Archive

R scripts for Analysis of Composition of Microbiomes (ANCOM).

Language: R - Size: 720 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

noriakis/ancom_lefse_comparison

Comparing ANCOM and LEfSe for differential abundance testing.

Language: Jupyter Notebook - Size: 213 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

noriakis/16S_Tools

Tools to process files related to 16S amplicon sequencing data.

Language: Python - Size: 4.88 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0