Man pages for pcahan1/CellNet
Assess and improve cell fate engineering with network biology

cleanupremove txt and trimmed.fq after running salmon
cn_addAUPRsutility function to compile cn_calcPRs
cn_applyApply CellNet to query data
cn_assessGRNassess performance of GRN predictions based on zscores. this...
cn_barplot_grnSingPlot GRN status
cn_barplot_grnSing_basebarplot this specific GRN
cn_calcPRsassess performance of GRN predictions based on zscores
cn_classAssessAssess classifiers based on validation data
cn_classifyclassify data
cn_class_perf_hm_orderedOrder classifier performance heatmap by description1 label of...
cn_clPerfdetermine performance of classification at given threshold
cn_clrmake a CLR-like matrix for assessment purposes
cn_compileGRNassessmentscompile results of assessing GRNs for multiple TFs
cn_computeAUCPRcompute AUPCR
cn_convertPRconvert a result of cn_calcPRs to something easily plot-able
cn_correctZmatmake Inf and -Inf values sensible
cn_evalrun cn_clPerf across thresholds
cn_extractRegsDFextracts the TRs, zscores, and corr values passing thresh
cn_extract_SN_DFreturns a DF of: sample_id, description, ctt, subnet_name,...
cn_extractSubNetsmake subnets from a GRN
cn_findSensAtreturn the sens at given FPR
cn_findSpecGenesfind genes that are preferentially expressed in specified...
cn_getRawGRNget raw GRN from zscores, and corr
cn_get_targetsget targets of a tf
cn_get_targets_ofget targets of tfs
cn_HmClassheatmap of the classification result
cn_HmClass_diseaseheatmap of gene expression for disease modeling studies Added...
cn_HmVarsheatmap of gene expression
cn_makeClassifiermake a single RF classifier
cn_make_grnReconstruct CT-specific GRNs
cn_make_processormake a CellNet object
cn_makeRFsmake classifiers
cn_makeSGsmake induced subgraphs from gene lists and iGraph object
cn_makeTFtableconvert a tf nis list to a DF
cn_MakeTLsget targets of tFs
cn_make_tValsEstimate gene expression dist in CTs
cn_make_tVals_predictcn_make_tVals_predict
cn_netScoresGRN status
cn_nisnetwork influence score
cn_nis_allNetwork Influence Score for all GRNs
cn_normalizeScoresNormalize grn status as compared to training data
cn_outputResWrite out classification scores, normalized data to csv
cn_rawScorecomputes the raw score for a gene as xmax-abs(zscore).
cn_rectAreacompute area of rect given by
cn_remake_processormake a CellNet object from an existing one with subset of...
cn_s3_fetchFastqFetch fastq files from S3
cn_salmonDerive gene expression estimates compatible with CellNet
cn_sampR_to_patternreturn a pattern for use in cn_testPattern (template...
cn_scoreGRN status
cn_setupset up directories on ephemeral drives that will be needed to...
cn_specGenesAllfinds general and context dependent specifc genes
cn_specGRNsextract sub-networks made up of CT genes;
cn_splitMakeAssessmake classifiers and assess
cn_summ_AUPRsprocesses result of cn_addAUPRs: p-value of fold...
cn_testPatterntemplate matching
cn_tfScoretranscription factor score
cn_trainNormFigure out normalization factors for GRNs, and norm training...
cn_writeReadmeHelper function to write a markdown line for the Readme
delete_pardelete files in parallel
downSampleWweighted subtraction from mapped reades
expr_readSampTabproperly read a csv file as a sampTab
expr_reorderre-order the sampTab, by dLevel, given dLevel names
fastq_readLengthDetermines read length of fastq file
fastq_trimTrim reads to specified length
feature_count_parcount the number of reads that overlap with genomic features
fetchAndConvertfetch sras and converts them to fastqs, can take a REALLY...
fetchIndexHandlerwrapper to fetch files needed to run salmon in case of errors
fetch_salmon_indicesfetch files needed to run salmon
find_tfsfind transcript factors
gene_expr_sumSum transcription expression estimates to gene-level...
geo_fixNamesreplace the files_names column with the actual files names,...
GEP_makeMeanrow average (or median) based on groups
get_grn_scoresInternal function, subset GRN scores for given sample indices
grn_corr_roundgene-gene correlations, and round
grn_zscorescompute CLR-like zscores
hisat_findIndicesfinds hisat indecies
hisat_QC_alignperforms qc on fastq file
hisat_QC_alignswrapper to hisat_QC_align
hsTFshuman transcriptional regulators
htseqCountcompiles read count hits
ig_tabToIgraphconvert a table to an igraph
mat_zscorescompute context dependent zscores
minDifmin diff
mmTFsmouse transcriptional regulators
mp_rainbowPlotmake a rainbow colored dot plot
multiplotCreate multiplot - adapted from Bioconductor package "scater"
Norm_cleanExpsummariz expression when there are multiple measures per gene...
Norm_cleanPropRawload and normalize each group separately, then return expProp...
Norm_loadAnnotationload the specified gene annotation table
Norm_preNormRawRun justRMA on samples, nor norm, just BG
Norm_quantNormquantile normalize expression matrix
ordered_class_perf_hmOutput ordered classifier performance heatmap by description1...
pdf_classification_hmAdded 6-4-18 Create pdf of classification heatmap, one column...
pdf_grn_statusCreate pdf of GRN status of starting and target cell types,...
pdf_grn_status_by_CTCreate pdf of GRN status plots, one plot with all dlevel...
pdf_grn_status_by_dlevelCreate pdf of GRN status plots, one plot with all C/T types...
pdf_nis_plotsCreate pdf of Network Influence Scores (NISs) for given C/T...
plot_class_PRsPlot results of cn_classAssess
plot_nisboxplot of network influence scores
pool_auPRspool auprs
processSRAprocesses a SRA study
qc_analysisRun qc pipeline
qcAndSalmonRuns the qc and salmon pipeline used by processSRA
randomizerandomize data matrix
s3_getget file from S3 using CLI
s3_listDirList directories in a bucket
s3_putput file from S3 using CLI
salmon_load_tranEstload Salmon-based transcript estimates
salmon_parquantify transcript levels using 'pseudo-alignments'
samp_for_classsplit data into train vs test
sample_profiles_grnsample equivalent numbers of profiles per cell type
sra_breakTablebreak a sample table into _inc_ size pieces
sra_deleteDeletes files with specified suffix in specified directory
sra_fetchfetch sras to path defined when configuring sra tools.
sra_parseunpacks the SRA files, splits them, and deletes SRAs
subsamp_fastqsrandomly samples reads from single end fastqs
subSamp_for_classselect from sample table
trans_dNormexpress as a fraction of the column total
trans_eShiftshift the expression of each sample so that the min=minVal
trans_fetch_indexget files needed to run Salmon and Hisat2 QC pipeline
trans_rnaseqweighted subtraction from mapped reades and log applied to...
utils_count_commentscount comments in a file
utils_loadObjectloads an R object when you don't know the name
utils_logmake a logging string
utils_myDateprint date
utils_myDist1-PCC distance
utils_strip_fnamereduces full path to filename
utils_stripwhitestrip whitespace from a string
utils_tarcompress_dirtars and compresses (gzip) dir
utils_unpackgzip and untar
weighted_downweighted subtraction from mapped reades, applied to all
pcahan1/CellNet documentation built on June 6, 2019, 11:55 p.m.