Showing 6 of total 6 results (show query)
bioc
tripr:T-cell Receptor/Immunoglobulin Profiler (TRIP)
TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.
Maintained by Nikolaos Pechlivanis. Last updated 5 months ago.
batcheffectmultiplecomparisongeneexpressionimmunooncologytargetedresequencingbioconductorclonotype
10.0 match 2 stars 5.48 score 4 scriptsbioc
VDJdive:Analysis Tools for 10X V(D)J Data
This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.
Maintained by Kelly Street. Last updated 5 months ago.
softwareimmunooncologysinglecellannotationrnaseqtargetedresequencingcpp
10.0 match 7 stars 5.32 score 1 scriptsbioc
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.
targetedresequencinggeneticsgenefusiondetectionsequencingbioconductor-packagecirculating-tumor-dnagene-fusionliquid-biopsynext-generation-sequencingtargeted-sequencingvariant-calling
10.0 match 3 stars 4.48 score 10 scriptsbioc
Clomial:Infers clonal composition of a tumor
Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.
Maintained by Habil Zare. Last updated 5 months ago.
geneticsgeneticvariabilitysequencingclusteringmultiplecomparisonbayesiandnaseqexomeseqtargetedresequencingimmunooncology
10.0 match 4.30 score 3 scriptsbioc
LymphoSeq:Analyze high-throughput sequencing of T and B cell receptors
This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.
Maintained by David Coffey. Last updated 5 months ago.
softwaretechnologysequencingtargetedresequencingalignmentmultiplesequencealignment
10.0 match 4.00 score 4 scriptsbioc
MDTS:Detection of de novo deletion in targeted sequencing trios
A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.
Maintained by Jack M.. Fu. Last updated 5 months ago.
statisticalmethodtechnologysequencingtargetedresequencingcoveragedataimport
10.0 match 2.78 score 1 scripts