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SCcaller / Single Cell Caller
Offers a validated protocol to accurately identify single-nucleotide variants (SNVs) across the genome from a single cell after whole-genome amplification (WGA). SCcaller is a single-cell-variant caller that was designed to adjust allelic amplification bias when estimating the likelihoods of three possibilities—artifact, heterozygous SNV and homozygous SNV for every candidate SNV locus. It also corrects for local allelic amplification bias in SNV calling.
SinCHet / SINgle Cell HETerogeneity
Can quantify cellular heterogeneity and identify novel candidate biomarkers. SinCHet is a MATLAB package with a graphical user interface (GUI) for visualization and user interaction, originally for cancer research but with the potential to be used for any single cell research. It provides unique insights into emerging or disappearing clones at different clonal resolutions between cell populations in different contexts. This method could be easily applied to compare heterogeneity between groups.
SAG-QC
Identifies and excludes non-target sequences independent of database. SAG-QC calculates the probability that a sequence was derived from contaminants by comparing k-mer compositions with the no template control sequences. It can determine bins of target sequences without any existing information. The tool is designed to exclude contaminant sequences from contigs. It can predict the distribution of target sequences accurately unless the single-amplified genome (SAG) sequences are extremely contaminated.
Conbase / CONfirming the allelic origin of BASEs
Calls clonal somatic mutations in genome sequencing data from single cells. Conbase identifies clonal somatic single nucleotide variants (sSNVs) with the aim of deciphering cell lineages in human beings. The software was designed with the goal to find a strategy to eliminate false variant calls in whole genome sequencing (WGS) data from amplified single cell DNA, for identifying variants that can be used to screen additional cells for the presence or absence of the somatic mutations.
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