First, cell events of each sample are grouped into individual clusters. ImmunoClust is an automated analysis pipeline for uncompensated fluorescence and mass cytometry data, which consists of two parts. Thus transferring the problem into that of one-class classification, as opposed to being an unsupervised learning problem. If CRISPR-associated (cas) genes are annotated the program will show them as well.įlowUtils provides a package with utilities for flow cytometry data.įlowQB is a fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.īased on comparison to fluorescence-minus-one the semi-automated algorithm helps in population discovery. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration.ĬRISPRs enables the detection of CRISPRs in locally-produced data and consultation of CRISPRs present in the database. Screening Bayesian Evaluation and Analysis Method (ScreenBEAM) is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data.Ī comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. MAGeCK outperforms existing computational methods in its control of the false discovery rate (FDR) and its high sensitivity. The workflow can be partitioned into four steps: read count normalization, mean-variance modeling, sgRNA ranking and gene ranking. MAGeCK identifies positively and negatively selected sgRNAs and genes in genome-scale CRISPR/Cas9 knockout experiments. Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout MAGeCK Its open virtual appliance allows analysis without prior programming knowledge and is therefore suited for novice and expert users. CaRpools integrates screening documentation and generation of standardized analysis reports. This web server allows specifying the characteristics and parameters of the nuclease to be used, although predefined set are available for several popular Cas proteins.ĬRISPR-AnalyzeR for pooled screens caRpoolsĬaRpools is an R package for exploratory data analysis providing CRISPR/Cas9 screen analysis. BreakingCas allows working with all eukaryotic genomes available in the ENSEMBL database, for a detailed inspection of the genomic neighbourhood of every single potential off-target so as to qualitatively assess them. Enhanced off-target prediction accuracy.īreaking CAS is a versatile system for detecting putative sgRNA off-targets in CRISPR/Cas applications.
CrispRVariants enables immediate comparison of variant spectra between target locations.ĬRISPOR assists with guide selection in 120 genomes, including plants and many emerging model organisms, and pre-calculated results for all human coding exons as a UCSC Genome Browser track. This toolkit can be easily used to create a variant allele summary plot and accompanying table of counts. CrispRVariants allows users to detect problems and filter sequences appropriately before estimating mutation efficiency. Individual variant alleles from either traditional Sanger sequencing or high-throughput CRISPR-Cas9 mutagenesis sequencing experiments can be quantified and visualized. Off spotter helps in the design of optimal "guide" RNAs (gRNAs) by providing several protospacer adjacent motif (PAM) choices, a run-time definition of the seed and of the allowed number of mismatches.ĬrispRVariants resolves and localizes individual mutant alleles with respect to the endonuclease cut site.
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