R-universe search: topic:next-generation-sequencing

Showing 5 of total 5 results (show query)

zhanxw

seqminer:Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.

Maintained by Xiaowei Zhan. Last updated 6 months ago.

annotation bcf bgen meta-analysis next-generation-sequencing plink sequencing tabix vcf workflow zlib bzip2 libzstd sqlite3 cpp

30 stars 8.29 score 111 scripts 6 dependents

bioc

epialleleR:Fast, Epiallele-Aware Methylation Caller and Reporter

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation.

Maintained by Oleksii Nikolaienko. Last updated 24 days ago.

dnamethylation epigenetics methylseq longread bioconductor dna-methylation epiallele next-generation-sequencing samtools curl bzip2 xz-utils zlib cpp

4 stars 5.94 score 5 scripts

bioc

ramr:Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

ramr is an R package for detection of epimutations (i.e., infrequent aberrant DNA methylation events) in large data sets obtained by methylation profiling using array or high-throughput methylation sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.

Maintained by Oleksii Nikolaienko. Last updated 23 days ago.

dnamethylation differentialmethylation epigenetics methylationarray methylseq aberrant-methylation bioconductor dna-methylation epimutation methylation-microarrays next-generation-sequencing cpp openmp

4.65 score 5 scripts

bioc

DNAfusion:Identification of gene fusions using paired-end sequencing

DNAfusion can identify gene fusions such as EML4-ALK based on paired-end sequencing results. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes.

Maintained by Christoffer Trier Maansson. Last updated 5 months ago.

targetedresequencing genetics genefusiondetection sequencing bioconductor-package circulating-tumor-dna gene-fusion liquid-biopsy next-generation-sequencing targeted-sequencing variant-calling

3 stars 4.48 score 10 scripts

bioc

rmspc:Multiple Sample Peak Calling

The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as "peaks"), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate samples are analyzed, overlapping peaks are expected. This repeated evidence can therefore be used to locally lower the minimum significance required to accept a peak. MSPC uses combined evidence from replicated experiments to evaluate peak calling output, rescuing peaks, and reduce false positives. It takes any number of replicates as input and improves sensitivity and specificity of peak calling on each, and identifies consensus regions between the input samples.

Maintained by Meriem Bahda. Last updated 6 days ago.

chipseq sequencing chiponchip dataimport rnaseq analysis chip-seq enriched-regions genome-analysis mspc next-generation-sequencing ngs-analysis overlapping-peaks peak peaks

20 stars 4.26 score 5 scripts