Man pages for mskilab/skitools
Various mskilab R utilties
| af | af |
| af2 | af2 |
| affine-map-methods | affine.map |
| alignment_metrics | alignment_metrics |
| allele_multiplicity | allele_multiplicity |
| all.paths | all.paths |
| alpha | alpha |
| anno.hops | anno.hops |
| arrstring | arrstring |
| bisort | bisort |
| blend | Blends colors |
| border | border |
| bplot | bplot |
| brew | brew |
| brewer.master | brewer.master |
| bsub_cmd | bsub_cmd |
| bubblemap | bubblemap |
| camerplot | cameraplot |
| capitalize | capitalize |
| cc | cc |
| ccf | ccf |
| charToDec | charToDec |
| chr2num | Convert from chrXX to numeric format |
| chron | chron |
| chunk | chunk |
| circos | circos Quick utility function for circos plot with read... |
| clock | clock times expression |
| clone_cluster | clone_cluster |
| collapse.paths | collapse.paths |
| col.scale | col.scale |
| col.slice | col.slice |
| contig.support | contig.support |
| cumseg | segment |
| d3igraph | d3igraph |
| dcast2 | dcast.data.table but allows vector arguments for value.var, |
| dd | dd |
| ddd | ddd |
| dedup | dedup |
| dev.all.off | dev.all.off |
| dflm | dflm |
| dfstring | dfstring |
| dirr | dirr |
| discordant.pairs | Label discordant read pairs |
| dmix | dmix |
| dodo.call | dodo.call |
| dot-e2class | .e2class |
| dplot | dplot |
| dtgr | Convert data.table to GRanges |
| dtt | dtt |
| du | du |
| dunlist | dunlist |
| edge2tip | edge2tip Returns matrix or data.table mapping edge to tips... |
| elcycles | elcycles |
| file.dir | file.dir |
| file.name | file.name |
| file.ready | file.ready |
| fill.blanks | fill.blanks |
| fisher.combined | fisher.combined |
| fisher.pairwise | fisher.pairwise |
| fisher.plot | Plots fisher contingency table with p value |
| flow_slurm_status | flow_slurm_status |
| fready | fread with name cleaning |
| fuckr | fuckr |
| func_code | func_code |
| gatk_callvariants | gatk_callvariants |
| gatk_haplotypecaller | gatk_haplotypecaller |
| gatk_oncotate | gatk_oncotate |
| gc_content | Get GC content from reference genome |
| get_dryclean_pon_path | get_dryclean_pon_path |
| get_dryclean_pon_template | get_dryclean_pon_template |
| get_gene_ampdels_from_jabba | get_gene_ampdels_from_jabba |
| get_gene_copy_numbers | get_gene_copy_numbers |
| get.pileup.gtrack | get.pileup.gtrack |
| get.var.col | Simple function storing default variant color scheme |
| ggjs | ggjs |
| gigs | gigs |
| gr2gatk | Dump GRanges to GATK file |
| gr2grl | gr2grl Quick way to make grl from list of indices into a... |
| gr2json | gr2json |
| gr.all | gr.all |
| gr.breaks | gr.breaks |
| gr.eval | gr.eval |
| gr.isclip | Check if reads are clipped |
| gr.isdisc | Checks if reads are discordant |
| grl.filter | Filters GRangesList to only include ranges in the specified... |
| grl.span | grl.span |
| grl.split | grl.split |
| gr.mincov | Return windows with minimal coverage |
| grok_bcf | Reads and parses bcf via bcftools call |
| grok_vcf | grok_vcf |
| gr.pad | Nice padding |
| gr.peaks | Find peaks in a 'GRanges' over a given meta-data field |
| gr.readfilter | Filter reads by average PHRED score Defines a cutoff score... |
| gr.refactor | gr.refactor |
| gr.round | Round a set of GRanges to another set "rounds" a set of query... |
| gr.tostring | gr.tostring |
| gsea_leading_edge | gsea_leading_edge |
| gstring | gstring |
| headf | headf |
| hets | Simple het "caller" meant to be used at validated het SNP... |
| html_link | html_link |
| html_tag | html_tag |
| igv | igv |
| igv_host | .igv_host |
| igv.loci | igv.loci Wrapper for igv function to dump table + screenshots... |
| img.html | img.html |
| img_link | img_link |
| import.ucsc | import.ucsc |
| ind2sub | ind2sub |
| install.packages.bioc | install.packages.bioc |
| install.packages.github | install.packages.github |
| internal | jabba.gwalk |
| is.dup | is.dup |
| jhom | wrapper around GxG homeology for junctions |
| junction.support | junction.support |
| karyoSim | karyoSim |
| kill.zombies | kill.zombies |
| label.runs | label.runs |
| ldim | ldim |
| levapply | levapply |
| lighten | lighten |
| list.expr | list.expr |
| loud | loud |
| lsos | lsos |
| maf2vcf | maf2vcf |
| maf_classify | maf_classify |
| maf_coding | maf_coding |
| maf_disp | maf_disp |
| maf_exonic | maf_exonic |
| maf_genic | maf_genic |
| maf_indel | maf_indel |
| maflite | maflite |
| maf_nonyn | maf_nonyn |
| maf_ns | maf_ns |
| maf_sub | maf_sub |
| maf_syn | maf_syn |
| maf_to_simple | maf_to_simple |
| maf_truncating | maf_truncating |
| match.bs | Identify matches between query and dictionary |
| match.seq | match.seq |
| memu | memu |
| mmatch | mmatch |
| modix | modix |
| morder | morder |
| more | more |
| mski_alpha | mski_alpha |
| mtable | mtable |
| muffle | muffle Runs code returning NULL is there is any error |
| multicoco | multicoco |
| munlist | munlist |
| mutclusters | mutclusters |
| mut_genecluster | mut_genecluster |
| mutpairsd | mutpairsd |
| mutrate_window | mutrate_window |
| nnnusvr | nnnusvr |
| nona | nona |
| nz | nz |
| oncoprint | oncoprint |
| oncotable | oncotable |
| oneoffs | Calls samtools mpileup to dump tsv of "one off" variants /... |
| padding | padding |
| parsesnpeff | parsesnpeff |
| phist | phist |
| pindel | pindel |
| plop | plop |
| plot.blank | plot.blank |
| plot_multiplicity | plot_multiplicity |
| pmGSEA | poor mans GSEA |
| pp2gb | pp2gb |
| ppdf | ppdf |
| ppgrid | ppgrid |
| ppng | ppng |
| PPplots | Plot bin and het copy number histogram as well as a contour... |
| preprocess_cov_for_dryclean | preprocess_cov_for_dryclean |
| print_eq | print_eq |
| process_gencode | process_gencode |
| pscatter | pscatter |
| qhost | qstat |
| qq_pval | qq plot given input p values |
| qq_repel | QQ plot with repel |
| qstat | qstat |
| query_lsf_out | query_lsf_out |
| queues | queues |
| quickSig | quickSig |
| qviz | qviz |
| ra_breaks | ra_breaks |
| ra.overlaps | identifies events that are in ra1 that do not exist in ra2.... |
| ra.union | ra.union |
| read.delim.cat | read.delim.cat |
| read_hg | Wrapper around BSgenome call |
| read_pon_dict | read_pon_dict |
| readRDA | readRDA |
| reads.to.walks | reads.to.walks |
| rel2abs | rel2abs |
| relib | relib |
| reorder_maf | reorder_maf |
| rmix | rmix |
| row.slice | row.slice |
| rpipe | read pipe readsLines from pipe and then closes the pipe |
| rr | rr |
| rrbind | rrbind |
| rrbind2 | Improved rbidn for intersecting columns of data.frames or... |
| sc.context | sc.context |
| score.walks | score.walks |
| seconds | seconds |
| seqinfo2gr | Create GRanges from Seqinfo |
| set.comp | set.comp |
| setxor | setxor |
| sgrep | System grep |
| sgrepl | System grep logical |
| slurm_dt | slurm_dt |
| sortable | sortable |
| sparse_subset | sparse_subset |
| splot | splot |
| spmelt | sparse matrix melt |
| ssegment | wrapper around DNAcopy to segment a coverage profile |
| sstat | sstat |
| standardize_segs | standardize_segs |
| stavePDF | stavePDF |
| staveRDS | staveRDS |
| strsplit2 | strsplit2 |
| strsplit.fwf | splits a single string according to fixed widths contained in... |
| sub2ind | sub2ind |
| system.call | Wrapper to base 'system' function to call system (e.g. perl)... |
| tabstring | tabstring |
| tailf | tailf |
| timestamp | timestamp |
| toggle_grfo | toggle data.table vs IRanges find overlaps |
| ucount | ucount |
| vaggregate | vaggregate |
| variants | variants |
| vplot | vplot |
| wfplot | Quick waterfall plot |
| which.char | which.char |
| wij | wij |
| wijj | wijj |
| write_ggjs | dumps ggjs formatted csv file from GRanges |
| write.htab | write.htab |
| write.tab | write.tab writes tab delimited no quotes without row names... |
