Showing 9 of total 9 results (show query)
bioc
xcms:LC-MS and GC-MS Data Analysis
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Maintained by Steffen Neumann. Last updated 16 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
196 stars 14.31 score 984 scripts 11 dependentsbioc
chromVAR:Chromatin Variation Across Regions
Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.
Maintained by Alicia Schep. Last updated 5 months ago.
singlecellsequencinggeneregulationimmunooncologycpp
7.31 score 772 scriptsbioc
PROcess:Ciphergen SELDI-TOF Processing
A package for processing protein mass spectrometry data.
Maintained by Xiaochun Li. Last updated 5 months ago.
immunooncologymassspectrometryproteomics
6.04 score 552 scriptsbioc
flowDensity:Sequential Flow Cytometry Data Gating
This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.
Maintained by Mehrnoush Malek. Last updated 5 months ago.
bioinformaticsflowcytometrycellbiologyclusteringcancerflowcytdatadatarepresentationstemcelldensitygating
5.17 score 83 scripts 3 dependentsbioc
GUIDEseq:GUIDE-seq and PEtag-seq analysis pipeline
The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.
Maintained by Lihua Julie Zhu. Last updated 5 months ago.
immunooncologygeneregulationsequencingworkflowstepcrispr
4.23 score 14 scripts
cran
monitoR:Acoustic Template Detection in R
Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.
Maintained by Sasha D. Hafner. Last updated 7 years ago.
3 stars 3.95 score 5 dependentsbioc
transcriptR:An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
The differences in the RNA types being sequenced have an impact on the resulting sequencing profiles. mRNA-seq data is enriched with reads derived from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial broader coverage of both exonic and intronic regions. The presence of intronic reads in GRO-seq type of data makes it possible to use it to computationally identify and quantify all de novo continuous regions of transcription distributed across the genome. This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events. Furthermore, the integration of ChIP- and RNA-seq data allows the identification all known and novel active transcription start sites within a given sample.
Maintained by Armen R. Karapetyan. Last updated 5 months ago.
immunooncologytranscriptionsoftwaresequencingrnaseqcoverage
3.30 score 2 scriptsbioc
BasicSTARRseq:Basic peak calling on STARR-seq data
Basic peak calling on STARR-seq data based on a method introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17.
Maintained by Annika Buerger. Last updated 5 months ago.
peakdetectiongeneregulationfunctionalpredictionfunctionalgenomicscoverage
3.30 score 1 scripts
rickhelmus
KPIC:Mass Spectrometry-Based Metabolomics Using Pure Ion Chromatograms
KPIC2 is an effective platform for LC-MS based metabolomics using pure ion chromatograms, which is developed for metabolomics studies. KPIC2 can detect pure ions accurately, align PICs across samples, group PICs to annotate isotope and adduct PICs, fill missing peaks and pattern recognition. High-resolution mass spectrometers like TOF and Orbitrap are more suitable.
Maintained by Hongchao Ji. Last updated 2 years ago.
1.70 score 3 scripts