Man pages for chris-hsiung/bears01
What the Package Does (One Line, Title Case)
| assembleCas9DualgRNALibraryOligo | Function to facilitate assembly of oligo pool synthesis for... |
| calculate_quantilethresperc | Calculate Quantile Threshold Percentages And Counts |
| clean_name | Clean Name |
| copy_to_global | Copy Variables from One Environment to the Global Environment |
| countBlpI | sum total occurrence of sites for a dsDNA sequence (input one... |
| countBsmBI | sum total occurrence of sites for a dsDNA sequence (input one... |
| countBstXI | sum total occurrence of sites for a dsDNA sequence (input one... |
| fasta2df | wrapper for seqinr::read.fasta |
| fasta2targetsites | By Chris Hsiung 2022-02-15 |
| flowjo2df | Function to read csv file exported from flowjo. The original... |
| getBestCRISPickSpacers | Get Best CRISPick Spacers. As written is currently intended... |
| getBothStrandsFASTA | by Chris Hsiung, updated 2022-02-15 |
| getCas9gRNAoligos_BstxIBlpI | for designing oligos to be cloned into BstxI/BlpI site (e.g.... |
| getGammaScore | This function calculates gamma from screen raw read counts |
| gethammingdist | function for getting the hamming distance between 2 strings |
| getHumanBiomaRt | wrapper for getting ensemblID association with gene symbols... |
| getLibraryOligoCas12a6plexgRNA | Function to assemble oligo for pooled synthesis for Cas12a... |
| getLibraryOligoCas12aDoublegRNA | Function to assemble oligo for pooled synthesis for Cas12a... |
| getLibraryOligoCas12aSinglegRNA | Function to assemble oligo for pooled synthesis for Cas12a... |
| getLibraryOligoCas12aTriplegRNA | Function to assemble oligo for pooled synthesis for Cas12a... |
| getOligosCas12a4plexgRNAVariantDR_BsmbI | for individually cloning Cas12a 4-plex spacer array into... |
| getOligosCas12a5plexgRNAVariantDR_BsmbI | for individually cloning Cas12a 5-plex spacer array into... |
| getOligosCas12a6plexgRNAVariantDR_BsmbI | for individually cloning Cas12a 6-plex spacer array into... |
| getOligosCas12aDualgRNA_BsmbI | for cloning double spacer into vector with BsmBI site (e.g.... |
| getOligosCas12aSinglegRNA_BsmbI | for cloning single spacer into vector with BsmBI site... |
| getOligosCas12aTriplegRNALbDR_BsmbI | for individually cloning Cas12a triple spacer array using Lb... |
| getOligosCas12aTriplegRNAVariantAsDR_BsmbI | for individually cloning Cas12a triple spacer array into... |
| getReverseComplement | Wrapper for Biostring::reverseComplement() |
| getSpacersForGeneByRank | for given gene retrieve top rows corresponding to (number of... |
| getTargetSites | Function to extract target sites for each sequence sequence... |
| plothalfviolin_withthres | Plot Half Violin with Thresholds |
| plotscatter_withthres | Scatter Plot with Thresholds and Quadrant Statistics |
| plotsplitviolin_withthres | Plot Split Violin with Thresholds |
| processFlowjoExportDir | Function to batch process .csv files (containing the... |
| propensityscore_multimatch | Propensity Score Matching for Multiple Control Groups |
| proptestfordf | Proportion Test for Two Groups in a DataFrame |
| removeBadCRISPickSpacers | Function reads CRISPick results as data frame and remove... |
| RNAfold2df | Function to parse the output from RNAfold 2.4.18 into data... |
| subsample_groupeddf | Subsample a Data Frame |
| ttestfordf | t Test for Two Groups in a DataFrame |
| wilcoxtestfordf | Wilcoxon Test for Two Groups in a DataFrame |
| writedf2fasta | wrapper for seqinr::write.fasta that takes data frame as... |
