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bioc
infercnv:Infer Copy Number Variation from Single-Cell RNA-Seq Data
Using single-cell RNA-Seq expression to visualize CNV in cells.
Maintained by Christophe Georgescu. Last updated 5 months ago.
softwarecopynumbervariationvariantdetectionstructuralvariationgenomicvariationgeneticstranscriptomicsstatisticalmethodbayesianhiddenmarkovmodelsinglecelljagscpp
601 stars 10.92 score 674 scriptsbioc
GenomicOZone:Delineate outstanding genomic zones of differential gene activity
The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. It enables characterization of effects on multiple genes within adaptive genomic neighborhoods, which could arise from genome reorganization, structural variation, or epigenome alteration. It guarantees cluster optimality, linear runtime to sample size, and reproducibility. One can apply it on genome-wide activity measurements such as copy number, transcriptomic, proteomic, and methylation data.
Maintained by Hua Zhong. Last updated 5 months ago.
softwaregeneexpressiontranscriptiondifferentialexpressionfunctionalpredictiongeneregulationbiomedicalinformaticscellbiologyfunctionalgenomicsgeneticssystemsbiologytranscriptomicsclusteringregressionrnaseqannotationvisualizationsequencingcoveragedifferentialmethylationgenomicvariationstructuralvariationcopynumbervariation
4.00 scorebioc
FilterFFPE:FFPE Artificial Chimeric Read Filter for NGS data
This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.
Maintained by Lanying Wei. Last updated 5 months ago.
structuralvariationsequencingalignmentqualitycontrolpreprocessing
3.30 score 1 scripts