Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel" published in Science Advances.
The data are freely avaible at GEO.
| File | Description |
|---|---|
| HPC | |
| 0_common_functions.R | Functions used though out the study |
| 1_create_sampleInfoTab.R | Script which created information table holding all meta data about samples |
| 2_plotMappingStats_countsRDS.R | Script which plots mapping statistics of samples and creates Rds with integer counts |
| JTK_CYCLEv3.1.R | |
| 3_detectCycles.R | Script which performs detection of cycling genes in all tissues with use of JTK CYCLE |
| 6_LASSO.R | Script to perform LASSO regression on data |
| 7_NeuralNet.R | Script to perform NeuralNet regression on data |
| 8_zeitzeiger.R | Script to run ZeitZeiger on data |
| 9_MolecularTimeTable.R | Script to run molecular time table on data |
| 10_NN_Eval_parellel.R | Script to evaluate various configurations of neural net to detected physiological time |
| 10_NN_Eval_parellel.sh | Script - wrapper to run 10_NN_Eval_parellel.R |
| 10_PhysioTimePredModelsEval.R | Script to perform comparison of various models to detected physiological time |
| 10_PhysioTimePredMTTonDGRP.R | Estimation of physiological time of the static DGRP samples with use of molecular time table |
| 11_DEbetweenTissues.R | Script to perform detection of differential expression between different tissues |
| 11_DGRPoutliersVars.R | Script to |
| 12_inputsForHomer.R | Script to create input files for run of Homer |
| 13_motifEnrichPostProc.R | Script to perform postprocessing of Homer run |
| 17_create_sampleInfoTab_28233.R | |
| 18_plotMappingStats_28233.R | |
| 19_detectCycles_28233.R | |
| 20_compare_w_28233.R | |
| 33_dynGENIE3.R | |
| 35_compareNets_white_28233.R | |
| 36A_activity_fromRawData.R | |
| 37_variantsInDGRP-796.R | |
| 39_down_Cell_ChiP-seq.sh | |
| 40_trimMapDedupl_Cell_ChiP-seq.sh | |
| 41_mergeReps_Cell_ChIP-seq.sh | |
| 42_bigwigs_Cell_ChiP-seq.sh | |
| 43_geneBodyBed.R | |
| 44_plotPeaks_ChIP-seq.R | |
| 45_plotBaboonMouseCyclOrth.R | |
| 46_phaseShift.R | |
| drawNets2.R | |
| figures.R | |
| model_the_expression.R |