kekemook/analysis repository overview

⁠Summary

This container can be used for 1) building bioinformatics/biostatistics pipelines for Illumina microarray methylation data, e.g., Illumina MethylationEPIC array, and 2) analyze the resulting microarray data.

⁠Installed R packages:

RnBeads, RnBeads.hg19, RPMM, bio3d, MatrixEQTL, biomaRt, DMRcate, unixtools (for setting a temp directory in R), devtools, fastDummies, mediation, GEEmediate, irlba(fast SVD and PCA), metafor (meta-analysis, Cochran Q test),

minfi, glmnet, feather, data.table, stringr, hdi, mediation, robustbase, lavaan, and R.utils. ggcorrplot, lmtest, matrixStat, GEOquery, merDeriv, arrow (lz4), clubSandwich., BSgenome, bacon, ttScreening,

hexbin, optparse, patchwork, R.utils, tidyverse

ape (for phylogenetic tree analysis)

Haplin, genio, EpiDISH, pwrEWAS, bigsnpr.

[Minfi related packages for cell compositions] IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, FlowSorted.Blood.EPIC, ExperimentHub dmrff DMRcate + DMRcatedata

scatterplot3d

*note: openblas-serial used for BLAS/LAPACK.

⁠Installed Python packages:

numpy, pandas, pandas-plink, feather-format, GEOparse, and jupyter (/opt/miniconda3/envs/analysis/bin/jupyter).

tweepy, fastapi

*Note: the abovementioned python packages were stored in a conda environment named "analysis".

⁠Software for genotype data:

bcftools (/opt/miniconda3/envs/analysis/bin/bcftools or /opt/bcftools/bcftools), bgenix (/opt/miniconda3/envs/bgenix/bin/bgenix), regenie (/opt/miniconda3/envs/regenie/bin/regenie), tabix (/opt/miniconda3/envs/tabix/bin/tabix).

plink1.9-linux64-bit (/opt/plink), plink2 (/opt/plink2). shapeit2 (/opt/shapeit.v2.904.3.10.0-693.11.6.el7.x86_64) beagle (/opt/beagle/), and PRSice.

METAL (/opt/generic-)

⁠Software for genomic sequence data:

aliview (aliview), iqtree (/opt/iqtree-2.1.3-Linux/bin/iqtree2),

⁠Other software:

ghostscript (for generating the PDFs of RnBeads). tacl (/opt/miniconda3/envs/tsd/bin/tacl, for tsd-api-client)

⁠Cautions:

You may need to execute IRkernel::installspec() to launch R sessions through jupyter notebook. Please proceed the following instructions:

1. Start an interactive shell of Docker/Singularity (bash command: docker run -it --rm your_container bash or singularity shell your_container),

2. Launch an R session (bash command: R), and

3. Type IRkernel::installspec()