| aggregatetogenes | Aggregates pooled CRISPR screen sgRNA data to gene data |
| caRpools | CaRpools - CRISPR-AnalyzeR for pooled Screens |
| carpools.hitident | Visualization of hit analysis performed by Wilcox, DESeq2 and... |
| carpools.hit.overview | Analysis: Analysis of pooled CRISPR screening data using a... |
| carpools.hit.scatter | Plot: Plotting Scatters for hit candidate genes for all... |
| carpools.hit.sgrna | Plotting sgRNA effects for all candidate genes or single... |
| carpools.raw.genes | Plotting sgRNA phenotype effects of a given gene |
| carpools.read.count.vs | QC: Scatterplots of Read-Counts |
| carpools.read.depth | QC: Plot Sequencing Read Depth |
| carpools.read.distribution | QC: Plot Readcount Distribution |
| carpools.reads.genedesigns | QC: Plot representation of sgRNAs per gene |
| carpools.sgrna.table | Table Output of sgRNA effect and Target Sequence |
| carpools.waterfall.pval | Visualization of p-value distribution |
| check.caRpools | Test caRpools installation and dependent software |
| compare.analysis | Exporting Hit Candidate Gene Information |
| CONTROL1 | Read-count data for untreated sample, replicate 1 |
| CONTROL1.g | Read-count data for untreated sample, replicate 1 |
| CONTROL2 | Read-count data for untreated sample, replicate 2 |
| CONTROL2.g | Read-count data for untreated sample, replicate 2 |
| data.extract | Extracting sgRNA information from NGS FASTQ files to create... |
| d.CONTROL1 | Name of Read-count data for untreated sample, replicate 1 |
| d.CONTROL2 | Name of Read-count data for untreated sample, replicate 2 |
| d.TREAT1 | Name of Read-count data for treated sample, replicate 1 |
| d.TREAT2 | Name of Read-count data for treated sample, replicate 2 |
| final.table | CaRpools: Generating Table with Analysis Information from all... |
| generate.hits | Retrieving overlapping hits from caRpools analysis |
| gene.remove | Remove gene information from sgRNA data.frame |
| get.gene.info | Retrieving Gene Annotation and Gene Identifier Conversion... |
| libFILE | FASTA file containing als sgRNA target sequences and... |
| load.file | Load sgRNA NGS Data especially for caRpools |
| load.packages | Loading and Installing packages used for caRpools |
| referencefile | Name of fasta reference file without extension. |
| stat.DESeq | Analysis: DESeq2 Analysis of pooled CRISPR NGS data |
| stat.mageck | Analysis: Analysis of pooled CRISPR screening data using a... |
| stats.data | Calculating data set statistics |
| stat.wilcox | Analysis: Analysis of pooled CRISPR screening data using a... |
| TREAT1 | Read-count data for treated sample, replicate 1 |
| TREAT1.g | Read-count data for treated sample, replicate 1 |
| TREAT2 | Read-count data for treated sample, replicate 2 |
| TREAT2.g | Read-count data for treated sample, replicate 2 |
| unmapped.genes | sgRNAs without reads |
| use.caRpools | Starting caRpools eport generation from R console |
