Man pages for shijianasdf/BasicBioinformaticsAnalysisFromZhongShan
Launch Usual Clinical tool for Kind Yield
| AnnoEset | Annotate EsetList via bioconductor |
| AnnotateJournal | Annotate journal id via crawler |
| AnnotateStringPPI | Re-annotation for ppi network from STRING web |
| base_common.annot | latest annotation contains ENSEMBL and other information of... |
| base_Fastcornet | fast way to create a network plot and edge/node data based on... |
| base_Fastcornet2 | fast way to create a network plot and edge/node data based on... |
| base_Fastcorrplot | help fast to draw a corrplot with multiple styles available... |
| base_Fastcorrplot2.1 | correlation analysis limited one control marker |
| base_Fastextra | a fast way to extra part of elements in a vetor. |
| base_Fastgrep | A Fast grep when lots of pattern used |
| base_FastMINE | a fast way to do MINE correlation analysis. |
| base_FastPearson | Get correlation index from expression matrix |
| base_Fastpoint1 | fast way to make a point plot based on ggplot2 |
| base_FastUpset | Give a fast way to draw an Upset plot base on upsetR |
| base_filter.low | filtering lots of different dataset via lots of condition... |
| base_is.all.na | Test whether a vector consists with NA values only |
| base_is.one.na | Test whether a vector consists with at least one NA values. |
| base_load1 | load local .rda files by a pattern |
| base_Make.cormatrix | translation between cormatirx and related long data frame |
| base_MINEplot | a corrplot based on MINE cor matrix |
| base_Plus.library | Plus.library |
| base_Plus.order | run order() for lots of cols in a matrix |
| base_QuickStart | Run series R script automatically |
| base_saveFastcornet | Save the result of Fastcornet series function |
| base_set.default | help self-defined function to set default values |
| base_show.color | preview color vector |
| base_stringposition | find the position of a specified string pattern |
| base_subset2 | get a subset of a data frame |
| BeforeWGCNA | Before WGCNA |
| BI_BalanceSplit | split a data frame into balanced parts according to specified... |
| BI_bootstrap.lasso | bulid a bootstrap lasso model via exprs and design objects |
| BI_boxplot.genedata2 | quick way to draw boxplot for multiple markers. |
| BI_clinic.filters | clinic.filters |
| BI_co.matrix2 | co.matrix2 |
| BI_cox.optimized | help get a best model based on prognosis information via Cox... |
| BI_cox.optimized3 | select prognosis-predictive genes |
| BI_cox.optimized4 | get survival significant markers based on KM-Curve data |
| BI_cox.threshold3 | Get a comprimized cut-off for survival analysis among mutiple... |
| BI_edgeR1 | Differencially expression analysis via edgeR package |
| BI_ensemblGo | Annotate the ENSG id with GO terms via ensembl online |
| BI_ensemblGoEnrich | Go annotation based on lucky::ensemblGo |
| BI_extra.surv | Get survival data of a gene based on expression and design... |
| BI_FastCoxlasso | Penalized Cox regression model via lasso algrithm |
| BI_FPKMtoTPM | FPKM value converted to TPM value |
| BI_genename.stad | gene names from TCGA-STAD with available annotation. |
| BI_getexpr | get long data frame from a gene expression matrix. |
| BI_heatmap.dds | heatmap.dds |
| BI_heatmap.dds2 | a quick way to draw heatmap |
| BI_pair.PSM | pair.PSM |
| BI_pair.random | pair.random |
| BI_result.DEG | Get a summary result from multiple DEGList |
| BI_result.lassoModel | Get results from lasso model function |
| BI_result.ROCList | show the progonis value of multiple model genes from ROCList... |
| BI_ROC.lasso | Bulid a binomial lasso model via exprs and design objects |
| BI_ROC.optimized | Common ROC optimized via AUC |
| BI_rowScale | rowScale |
| BI_sametrend | find out genes that can be plot appropriately in boxplot with... |
| BI_select.eset | fast way to select eset |
| boxplot_genedata | Fast way to draw boxplot for gene expression |
| ceRNAData | Get lnRNA-miRNA/mRNA-miRNA interaction from starBase |
| ceRNANet | Get ceRNA network from starBase 3.0 by giving miRNAs symbol |
| classify | Classify a vector by specified classifier |
| clinic_CreateTableOne2 | Optimized baselined information production from tableone... |
| clinic_getCoxTable | get a model result of univariate and multivariate Cox... |
| combn2 | get all arrage for given n and k |
| compareROC | Produce time dependent KM-ROC curves |
| compareROC2 | get ROC Curve of one or more variates for a binary status |
| convert | multiple annotation based on dataset common.annot. |
| convertStatus | convertStatus |
| CorrectTNM | Version control for TCGA TNM stage |
| cox.optimized2 | A pipline of lasso cox modeling |
| CreateBioProject | Create a bioproject with constant format |
| cut_vector | cut a vector into lots of parts |
| data_fpkm | a simple dataset of fpkm values |
| data_journals | SCI journals dataset |
| DESeq1 | Standard process for DESeq2 RNA-Seq differencial expression... |
| exampleLassoCox | Visualize and analysis of cox.optimized2 result by giving a... |
| fa.annotate | annotate probe sequence via fasta object |
| FastBar | Fast Way to Get a Bar plot based on ggpubr |
| Fastboxplot | fast way to draw a boxplot based on ggplot2 |
| FastCeRNA | easy ceRNA network via GDCRNATools::gdcCEAnalysis |
| FastCeRNA_edge | Get miRNA-lncRNA-mRNA edge data after FastCeRNA |
| FastCeRNA_edge2 | a simple method for ceRNA network edge/node selection |
| Fastcornet2 | Draw Network plot of D3 style |
| FastEnrichPlot | Fast way to draw enrich plot after clusterProfilter... |
| FastGO | GO analysis via clusterProfiler package |
| FastGSEA | Fast way to do GSEA for a geneList object |
| FastKEGG | KEGG analysis via clusterProfiler package |
| FastMS | Fast Molecular Signatures Analysis via clusterProfilter |
| FastQPCR | Fast way to deal with results of qRT-PCR |
| FastScore | Fast way to calculate scores for multiple markers |
| FastSurvplot | Fast way to draw a KM plot of ggplot style |
| FastWGCNA | Standard pipeline for WGCNA |
| FastWGCNA_network | Visualize specified module Network after FastWGCNA pipeline |
| GEO_AddDesignList | AddDesignList |
| GEO_AnnotateDesignEset | AnnotateDesignEset |
| GEO_boxplot.DE | quick way to draw a boxplot for specified contrast via... |
| GEO_boxplot.MA | quick way to draw a boxplot for specified contrast via MAList... |
| GEO_getElist | getElist |
| GEO_getOneDesignEset | get one DesignEset |
| GEO_MApipeline | transform a raw MA object to a comparable MA which is needed... |
| geom_cake | geom_cake |
| geom_flat_violin | geom_flat_violin |
| geom_ord_ellipse | geom_ord_ellipse |
| GEO_QC.boxplot | QC.boxplot |
| GEO_QC.cluster | QC.cluster |
| GEO_QC.density | QC.density |
| GEO_QC.PCA | QC.PCA |
| GEO_QCplot | QCplot |
| GEO_QC.plotMA | QC.plotMA |
| getAnnotation | Get annotation from a gtf annotation file |
| getAnnotation2 | Get further annotation after getAnnotation() |
| get.fa.annoatation | create a powerful annotation object for chips containing... |
| get.ISSN | after get.journal.ISSN |
| get.ISSN2 | After get.ISSN |
| GetMEs | Get new module eigengenes matrix from a given dataset |
| getNomogram | Get nomogram,standard curves and return related data and... |
| getsearch | get search formula with specified journal names or ISSN |
| getTimeROC | time-dependent ROC curve base on timeROC package |
| GetWGCNATrait | create trait matrix for WGCNA |
| LuckyVerbose | easy report system in function building |
| MakeENlist | create ENote journal list .txt to help annotation in ENote... |
| ModuleHub | Enhanced hub genes exploration after FastWGCNA pipeline |
| ModulePreservation | a easy method for Module Preservation in FastWGCNA pipeline |
| ModuleSurv | Explore relationship between Modules and survival in... |
| ModuleSurvValid | Get module-Survival relationship given new validation cohorts |
| ModuleTrait | Enhanced Module-Trait Relationships Plot after FastWGCNA... |
| ModuleTraitValid | Get module-trait relationship given new validation cohorts |
| mymusic | play music via tuneR |
| Plus.library | Automatically install and library package |
| ProteinAnnotation | Get protein annotation from gpl file |
| round2 | publish-level round |
| ScreenGenes | DEGs screening via common t-test |
| SearchIF2 | SearchIF2:get journal list with specified strings of journal... |
| SeqmanAfter | extra information from match_probe.txt from Seqman software |
| SeqmanBefore | prepare chip probe information(.txt) before seqman pipelin |
| SequenceMotif | co-motif exploration for sequence |
| starBase1 | Data Clean for starBase |
| Survplot_genedata | Survival K-M plot base on expression matrix and design object |
| testBatchEffect | test and remove potencial batch effects |
| testFastBar | Fast Way to Get a Bar plot based on ggpubr |
| testPrimer | Give Mutiple primers,test the amplication sequence and... |
| testPrimer1 | Give a primer,test the amplication sequence and whether cross... |
| WesternBlotQuantity | Tool for protein quantity in Western Blot |
