knights-lab

Pinned Repositories

BugBase
Language:HTML35 10 1512
BURST
An ultrafast optimal aligner for mapping large NGS data to large genome databases.
Language:C57 5 358
dietstudy_analyses
Language:R10 4 09
Food_Tree
USDA Nutrition codes Tree
Language:R10 5 07
IMP_analyses
immigrant microbiome project related analyses
Language:R4 9 04
LMdist
LMdist is an unsupervised algorithm for correcting oversaturated pairwise distance and dissimilarity measures. Compatible with any pairwise beta diversity measure, LMdist will uncover underlying environmental gradients and resolve arches/horseshoes in ordination.
Language:R5 2 00
MLRepo
Language:R34 5 313
shi7
Auto-parameterizing QC Pipeline for Illumina sequencing runs
Language:Python18 11 597
SHOGUN
SHallow shOtGUN profiler
Language:Python54 8 3219
UTree
K-mer searching with trees
Language:C4 7 51

knights-lab's Repositories

knights-lab/BURST
An ultrafast optimal aligner for mapping large NGS data to large genome databases.
Language:C57 5 358
knights-lab/SHOGUN
SHallow shOtGUN profiler
Language:Python54 8 3219
knights-lab/MLRepo
Language:R34 5 313
knights-lab/shi7
Auto-parameterizing QC Pipeline for Illumina sequencing runs
Language:Python18 11 597
knights-lab/dietstudy_analyses
Language:R10 4 09
knights-lab/Food_Tree
USDA Nutrition codes Tree
Language:R10 5 07
knights-lab/LMdist
LMdist is an unsupervised algorithm for correcting oversaturated pairwise distance and dissimilarity measures. Compatible with any pairwise beta diversity measure, LMdist will uncover underlying environmental gradients and resolve arches/horseshoes in ordination.
Language:R5 2 00
knights-lab/IMP_analyses
immigrant microbiome project related analyses
Language:R4 9 04
knights-lab/UTree
K-mer searching with trees
Language:C4 7 51
knights-lab/climate-trace-shipping
Language:Jupyter Notebook2 2 01
knights-lab/ermin-standards
Emissions Report Minimum INformation (ERMIN) Standards
Language:Python2 2 111
knights-lab/aKronyMer
Ultrafast genome- and dataset-scale distance matrix and phylogenetic tree creation
Language:C1 2 01
knights-lab/analysis_SHOGUN
Analysis scripts and code for reproducing the analysis for the SHOGUN paper
Language:Jupyter Notebook1 7 161
knights-lab/analysis_tree
Language:Python11
knights-lab/conda-recipes
Conda recipes for the knights lab
Language:Python1 7 11
knights-lab/DOJO
Language:Python1 7 11
knights-lab/kafan
Lossless data compression codec specialized for sequence data
Language:C1 2 0
knights-lab/NINJA-utils
Reusable classes and configurations for easy Python package development.
Language:Python1 7 01
knights-lab/q2-ninja-ops
QIIME2 Plugin for NINJA-OPS
Language:Python1 4 13
knights-lab/analysis_italy
Language:Jupyter Notebook3 0
knights-lab/BetaDiv
Materials and analyses for "Microbiome beta diversity analyses and visualization." A discussion of beta diversity analysis methods, factors we must consider in each step, and how we might better use these methods in forthcoming microbiome research.
Language:R3 0
knights-lab/dietstudy
Diet Study
Language:JavaScript3 0
knights-lab/douc_gut_sites
Microbiome of red-shanked douc gut sites
Language:R1
knights-lab/foodworks
Experimenting with Bayesian Networks for predicting day-to-day microbiome fluctuations
Language:Jupyter Notebook3 0
knights-lab/helix
Short scripts for use within the knights-lab
Language:Python3 0
knights-lab/IMP-Open-Ref
Open Ref BURST with IMP data
Language:R2 0
knights-lab/knights-lab.github.io
Knights Lab website via Github pages
Language:JavaScript
knights-lab/MAGICstudy
The Microbiome, Antibiotics, and Growth Infant Cohort associated analyses.
Language:Jupyter Notebook2 0
knights-lab/megaperm
Two-group, two-timepoint non-parametric permutation-based significance testing allowing for uneven repeated sampling (whew!)
Language:R2 1
knights-lab/type_1
Language:Jupyter Notebook3 0