Files in pcahan1/CellNet

Assess and improve cell fate engineering with network biology

R/CellNet.R R/cn_assess.R R/cn_graphics.R R/cn_grn.R R/cn_preprocess.R R/cn_sc.R R/cn_utils.R R/data.R README.md man/GEP_makeMean.Rd man/Norm_cleanExp.Rd man/Norm_cleanPropRaw.Rd man/Norm_loadAnnotation.Rd man/Norm_preNormRaw.Rd man/Norm_quantNorm.Rd man/cleanup.Rd man/cn_HmClass.Rd man/cn_HmClass_disease.Rd man/cn_HmVars.Rd man/cn_MakeTLs.Rd man/cn_addAUPRs.Rd man/cn_apply.Rd man/cn_assessGRN.Rd man/cn_barplot_grnSing.Rd man/cn_barplot_grnSing_base.Rd man/cn_calcPRs.Rd man/cn_clPerf.Rd man/cn_classAssess.Rd man/cn_class_perf_hm_ordered.Rd man/cn_classify.Rd man/cn_clr.Rd man/cn_compileGRNassessments.Rd man/cn_computeAUCPR.Rd man/cn_convertPR.Rd man/cn_correctZmat.Rd man/cn_eval.Rd man/cn_extractRegsDF.Rd man/cn_extractSubNets.Rd man/cn_extract_SN_DF.Rd man/cn_findSensAt.Rd man/cn_findSpecGenes.Rd man/cn_getRawGRN.Rd man/cn_get_targets.Rd man/cn_get_targets_of.Rd man/cn_makeClassifier.Rd man/cn_makeRFs.Rd man/cn_makeSGs.Rd man/cn_makeTFtable.Rd man/cn_make_grn.Rd man/cn_make_processor.Rd man/cn_make_tVals.Rd man/cn_make_tVals_predict.Rd man/cn_netScores.Rd man/cn_nis.Rd man/cn_nis_all.Rd man/cn_normalizeScores.Rd man/cn_outputRes.Rd man/cn_rawScore.Rd man/cn_rectArea.Rd man/cn_remake_processor.Rd man/cn_s3_fetchFastq.Rd man/cn_salmon.Rd man/cn_sampR_to_pattern.Rd man/cn_score.Rd man/cn_setup.Rd man/cn_specGRNs.Rd man/cn_specGenesAll.Rd man/cn_splitMakeAssess.Rd man/cn_summ_AUPRs.Rd man/cn_testPattern.Rd man/cn_tfScore.Rd man/cn_trainNorm.Rd man/cn_writeReadme.Rd man/delete_par.Rd man/downSampleW.Rd man/expr_readSampTab.Rd man/expr_reorder.Rd man/fastq_readLength.Rd man/fastq_trim.Rd man/feature_count_par.Rd man/fetchAndConvert.Rd man/fetchIndexHandler.Rd man/fetch_salmon_indices.Rd man/find_tfs.Rd man/gene_expr_sum.Rd man/geo_fixNames.Rd man/get_grn_scores.Rd man/grn_corr_round.Rd man/grn_zscores.Rd man/hisat_QC_align.Rd man/hisat_QC_aligns.Rd man/hisat_findIndices.Rd man/hsTFs.Rd man/htseqCount.Rd man/ig_tabToIgraph.Rd man/mat_zscores.Rd man/minDif.Rd man/mmTFs.Rd man/mp_rainbowPlot.Rd man/multiplot.Rd man/ordered_class_perf_hm.Rd man/pdf_classification_hm.Rd man/pdf_grn_status.Rd man/pdf_grn_status_by_CT.Rd man/pdf_grn_status_by_dlevel.Rd man/pdf_nis_plots.Rd man/plot_class_PRs.Rd man/plot_nis.Rd man/pool_auPRs.Rd man/processSRA.Rd man/qcAndSalmon.Rd man/qc_analysis.Rd man/randomize.Rd man/s3_get.Rd man/s3_listDir.Rd man/s3_put.Rd man/salmon_load_tranEst.Rd man/salmon_par.Rd man/samp_for_class.Rd man/sample_profiles_grn.Rd man/sra_breakTable.Rd man/sra_delete.Rd man/sra_fetch.Rd man/sra_parse.Rd man/subSamp_for_class.Rd man/subsamp_fastqs.Rd man/trans_dNorm.Rd man/trans_eShift.Rd man/trans_fetch_index.Rd man/trans_rnaseq.Rd man/utils_count_comments.Rd man/utils_loadObject.Rd man/utils_log.Rd man/utils_myDate.Rd man/utils_myDist.Rd man/utils_strip_fname.Rd man/utils_stripwhite.Rd man/utils_tarcompress_dir.Rd man/utils_unpack.Rd man/weighted_down.Rd newHm.R