| cleanup | remove txt and trimmed.fq after running salmon |
| cn_addAUPRs | utility function to compile cn_calcPRs |
| cn_apply | Apply CellNet to query data |
| cn_assessGRN | assess performance of GRN predictions based on zscores. this... |
| cn_barplot_grnSing | Plot GRN status |
| cn_barplot_grnSing_base | barplot this specific GRN |
| cn_calcPRs | assess performance of GRN predictions based on zscores |
| cn_classAssess | Assess classifiers based on validation data |
| cn_classify | classify data |
| cn_class_perf_hm_ordered | Order classifier performance heatmap by description1 label of... |
| cn_clPerf | determine performance of classification at given threshold |
| cn_clr | make a CLR-like matrix for assessment purposes |
| cn_compileGRNassessments | compile results of assessing GRNs for multiple TFs |
| cn_computeAUCPR | compute AUPCR |
| cn_convertPR | convert a result of cn_calcPRs to something easily plot-able |
| cn_correctZmat | make Inf and -Inf values sensible |
| cn_eval | run cn_clPerf across thresholds |
| cn_extractRegsDF | extracts the TRs, zscores, and corr values passing thresh |
| cn_extract_SN_DF | returns a DF of: sample_id, description, ctt, subnet_name,... |
| cn_extractSubNets | make subnets from a GRN |
| cn_findSensAt | return the sens at given FPR |
| cn_findSpecGenes | find genes that are preferentially expressed in specified... |
| cn_getRawGRN | get raw GRN from zscores, and corr |
| cn_get_targets | get targets of a tf |
| cn_get_targets_of | get targets of tfs |
| cn_HmClass | heatmap of the classification result |
| cn_HmClass_disease | heatmap of gene expression for disease modeling studies Added... |
| cn_HmVars | heatmap of gene expression |
| cn_makeClassifier | make a single RF classifier |
| cn_make_grn | Reconstruct CT-specific GRNs |
| cn_make_processor | make a CellNet object |
| cn_makeRFs | make classifiers |
| cn_makeSGs | make induced subgraphs from gene lists and iGraph object |
| cn_makeTFtable | convert a tf nis list to a DF |
| cn_MakeTLs | get targets of tFs |
| cn_make_tVals | Estimate gene expression dist in CTs |
| cn_make_tVals_predict | cn_make_tVals_predict |
| cn_netScores | GRN status |
| cn_nis | network influence score |
| cn_nis_all | Network Influence Score for all GRNs |
| cn_normalizeScores | Normalize grn status as compared to training data |
| cn_outputRes | Write out classification scores, normalized data to csv |
| cn_rawScore | computes the raw score for a gene as xmax-abs(zscore). |
| cn_rectArea | compute area of rect given by |
| cn_remake_processor | make a CellNet object from an existing one with subset of... |
| cn_s3_fetchFastq | Fetch fastq files from S3 |
| cn_salmon | Derive gene expression estimates compatible with CellNet |
| cn_sampR_to_pattern | return a pattern for use in cn_testPattern (template... |
| cn_score | GRN status |
| cn_setup | set up directories on ephemeral drives that will be needed to... |
| cn_specGenesAll | finds general and context dependent specifc genes |
| cn_specGRNs | extract sub-networks made up of CT genes; |
| cn_splitMakeAssess | make classifiers and assess |
| cn_summ_AUPRs | processes result of cn_addAUPRs: p-value of fold... |
| cn_testPattern | template matching |
| cn_tfScore | transcription factor score |
| cn_trainNorm | Figure out normalization factors for GRNs, and norm training... |
| cn_writeReadme | Helper function to write a markdown line for the Readme |
| delete_par | delete files in parallel |
| downSampleW | weighted subtraction from mapped reades |
| expr_readSampTab | properly read a csv file as a sampTab |
| expr_reorder | re-order the sampTab, by dLevel, given dLevel names |
| fastq_readLength | Determines read length of fastq file |
| fastq_trim | Trim reads to specified length |
| feature_count_par | count the number of reads that overlap with genomic features |
| fetchAndConvert | fetch sras and converts them to fastqs, can take a REALLY... |
| fetchIndexHandler | wrapper to fetch files needed to run salmon in case of errors |
| fetch_salmon_indices | fetch files needed to run salmon |
| find_tfs | find transcript factors |
| gene_expr_sum | Sum transcription expression estimates to gene-level... |
| geo_fixNames | replace the files_names column with the actual files names,... |
| GEP_makeMean | row average (or median) based on groups |
| get_grn_scores | Internal function, subset GRN scores for given sample indices |
| grn_corr_round | gene-gene correlations, and round |
| grn_zscores | compute CLR-like zscores |
| hisat_findIndices | finds hisat indecies |
| hisat_QC_align | performs qc on fastq file |
| hisat_QC_aligns | wrapper to hisat_QC_align |
| hsTFs | human transcriptional regulators |
| htseqCount | compiles read count hits |
| ig_tabToIgraph | convert a table to an igraph |
| mat_zscores | compute context dependent zscores |
| minDif | min diff |
| mmTFs | mouse transcriptional regulators |
| mp_rainbowPlot | make a rainbow colored dot plot |
| multiplot | Create multiplot - adapted from Bioconductor package "scater" |
| Norm_cleanExp | summariz expression when there are multiple measures per gene... |
| Norm_cleanPropRaw | load and normalize each group separately, then return expProp... |
| Norm_loadAnnotation | load the specified gene annotation table |
| Norm_preNormRaw | Run justRMA on samples, nor norm, just BG |
| Norm_quantNorm | quantile normalize expression matrix |
| ordered_class_perf_hm | Output ordered classifier performance heatmap by description1... |
| pdf_classification_hm | Added 6-4-18 Create pdf of classification heatmap, one column... |
| pdf_grn_status | Create pdf of GRN status of starting and target cell types,... |
| pdf_grn_status_by_CT | Create pdf of GRN status plots, one plot with all dlevel... |
| pdf_grn_status_by_dlevel | Create pdf of GRN status plots, one plot with all C/T types... |
| pdf_nis_plots | Create pdf of Network Influence Scores (NISs) for given C/T... |
| plot_class_PRs | Plot results of cn_classAssess |
| plot_nis | boxplot of network influence scores |
| pool_auPRs | pool auprs |
| processSRA | processes a SRA study |
| qc_analysis | Run qc pipeline |
| qcAndSalmon | Runs the qc and salmon pipeline used by processSRA |
| randomize | randomize data matrix |
| s3_get | get file from S3 using CLI |
| s3_listDir | List directories in a bucket |
| s3_put | put file from S3 using CLI |
| salmon_load_tranEst | load Salmon-based transcript estimates |
| salmon_par | quantify transcript levels using 'pseudo-alignments' |
| samp_for_class | split data into train vs test |
| sample_profiles_grn | sample equivalent numbers of profiles per cell type |
| sra_breakTable | break a sample table into _inc_ size pieces |
| sra_delete | Deletes files with specified suffix in specified directory |
| sra_fetch | fetch sras to path defined when configuring sra tools. |
| sra_parse | unpacks the SRA files, splits them, and deletes SRAs |
| subsamp_fastqs | randomly samples reads from single end fastqs |
| subSamp_for_class | select from sample table |
| trans_dNorm | express as a fraction of the column total |
| trans_eShift | shift the expression of each sample so that the min=minVal |
| trans_fetch_index | get files needed to run Salmon and Hisat2 QC pipeline |
| trans_rnaseq | weighted subtraction from mapped reades and log applied to... |
| utils_count_comments | count comments in a file |
| utils_loadObject | loads an R object when you don't know the name |
| utils_log | make a logging string |
| utils_myDate | print date |
| utils_myDist | 1-PCC distance |
| utils_strip_fname | reduces full path to filename |
| utils_stripwhite | strip whitespace from a string |
| utils_tarcompress_dir | tars and compresses (gzip) dir |
| utils_unpack | gzip and untar |
| weighted_down | weighted subtraction from mapped reades, applied to all |
