Showing 12 of total 12 results (show query)
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
PureCN:Copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.
Maintained by Markus Riester. Last updated 1 days ago.
copynumbervariationsoftwaresequencingvariantannotationvariantdetectioncoverageimmunooncologybioconductor-packagecell-free-dnacopy-numberlohtumor-heterogeneitytumor-mutational-burdentumor-purity
132 stars 9.88 score 40 scriptsbioc
Rsubread:Mapping, quantification and variant analysis of sequencing data
Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.
Maintained by Wei Shi. Last updated 9 days ago.
sequencingalignmentsequencematchingrnaseqchipseqsinglecellgeneexpressiongeneregulationgeneticsimmunooncologysnpgeneticvariabilitypreprocessingqualitycontrolgenomeannotationgenefusiondetectionindeldetectionvariantannotationvariantdetectionmultiplesequencealignmentzlib
9.24 score 892 scripts 10 dependentsbioc
CrispRVariants:Tools for counting and visualising mutations in a target location
CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.
Maintained by Helen Lindsay. Last updated 5 months ago.
immunooncologycrisprgenomicvariationvariantdetectiongeneticvariabilitydatarepresentationvisualizationsequencing
5.51 score 32 scriptsbioc
lineagespot:Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.
Maintained by Nikolaos Pechlivanis. Last updated 5 months ago.
variantdetectionvariantannotationsequencing
2 stars 5.15 score 4 scriptsbioc
scQTLtools:An R package for single-cell eQTL analysis and visualization
This package specializes in analyzing and visualizing eQTL at the single-cell level. It can read gene expression matrices or Seurat data, or SingleCellExperiment object along with genotype data. It offers a function for cis-eQTL analysis to detect eQTL within a given range, and another function to fit models with three methods. Using this package, users can also generate single-cell level visualization result.
Maintained by Xiaofeng Wu. Last updated 3 days ago.
softwaregeneexpressiongeneticvariabilitysnpdifferentialexpressiongenomicvariationvariantdetectiongeneticsfunctionalgenomicssystemsbiologyregressionsinglecellnormalizationvisualizationrna-seqsc-eqtl
3 stars 5.02 scorebioc
RVS:Computes estimates of the probability of related individuals sharing a rare variant
Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).
Maintained by Alexandre Bureau. Last updated 5 months ago.
immunooncologygeneticsgenomewideassociationvariantdetectionexomeseqwholegenome
4.78 score 9 scriptsbioc
svaRetro:Retrotransposed transcript detection from structural variants
svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.
Maintained by Ruining Dong. Last updated 5 months ago.
dataimportsequencingannotationgeneticsvariantannotationcoveragevariantdetection
4.60 score 4 scriptsbioc
panelcn.mops:CNV detection tool for targeted NGS panel data
CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.
Maintained by Gundula Povysil. Last updated 5 months ago.
sequencingcopynumbervariationcellbiologygenomicvariationvariantdetectiongenetics
4.08 score 12 scriptsbioc
MADSEQ:Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.
Maintained by Yu Kong. Last updated 5 months ago.
genomicvariationsomaticmutationvariantdetectionbayesiancopynumbervariationsequencingcoveragejagscpp
4 stars 3.60 score 1 scriptsbioc
SICtools:Find SNV/Indel differences between two bam files with near relationship
This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.
Maintained by Xiaobin Xing. Last updated 5 months ago.
alignmentsequencingcoveragesequencematchingqualitycontroldataimportsoftwaresnpvariantdetection
3.30 score 1 scriptsbioc
appreci8R:appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.
Maintained by Sarah Sandmann. Last updated 5 months ago.
variantdetectiongeneticvariabilitysnpvariantannotationsequencing
3.30 score 1 scripts