:: DESCRIPTION
FIXSEQ is a over-dispersion correction technique that serves as a smarter way to de-duplicate counts.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hashimoto TB, Edwards MD, Gifford DK.
Universal count correction for high-throughput sequencing.
PLoS Comput Biol. 2014 Mar 6;10(3):e1003494. doi: 10.1371/journal.pcbi.1003494. PMID: 24603409; PMCID: PMC3945112.
:: DESCRIPTION
dd_detection is a tool for finding dispersed duplications (DDs) in high throughput sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Detecting Dispersed Duplications in High-Throughput Sequencing Data using a Database-Free Approach.
Kroon M, Lameijer EW, Lakenberg N, Hehir-Kwa JY, Thung DT, Slagboom PE, Kok JN, Ye K.
Bioinformatics. 2015 Oct 27. pii: btv621.
:: DESCRIPTION
bcbio-nextgen is a python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
HTSeq–a Python framework to work with high-throughput sequencing data.
Anders S, Pyl PT, Huber W.
Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638.
:: DESCRIPTION
ChIPseqR is an algorithm for the analysis of nucleosome positioning and histone modification ChIP-seq experiments.
::DEVELOPER
CSIRO Transformational Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ChIPseqR: analysis of ChIP-seq experiments.
Humburg P, Helliwell CA, Bulger D, Stone G.
BMC Bioinformatics. 2011 Jan 31;12:39. doi: 10.1186/1471-2105-12-39.
:: DESCRIPTION
BTP (Binary Tree Partition)is a novel combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.
Hajirasouliha I, Mahmoody A, Raphael BJ.
Bioinformatics. 2014 Jun 15;30(12):i78-86. doi: 10.1093/bioinformatics/btu284.
:: DESCRIPTION
QuantumClone is a clonal reconstruction method for whole genome or whole exome sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Deveau P, et al.
QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.
Bioinformatics. 2018 Jun 1;34(11):1808-1816. doi: 10.1093/bioinformatics/bty016. PMID: 29342233; PMCID: PMC5972665.
:: DESCRIPTION
REDseq includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.
::DEVELOPER
Program in Gene Function and Expression@umassmed
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Chen PB, Zhu LJ, Hainer SJ, McCannell KN, Fazzio TG.
Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo.
BMC Genomics. 2014 Dec 15;15(1):1104. doi: 10.1186/1471-2164-15-1104. PMID: 25494698; PMCID: PMC4378318.
:: DESCRIPTION
pRESTO (REpertoire Sequencing TOolkit) is an integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.
Vander Heiden JA, Yaari G, Uduman M, Stern JN, O’Connor KC, Hafler DA, Vigneault F, Kleinstein SH.
Bioinformatics. 2014 Mar 26.
:: DESCRIPTION
GPSeq is a software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
A two-parameter generalized Poisson model to improve the analysis of RNA-seq data.
Srivastava S, Chen L.
Nucleic Acids Res. 2010 Sep;38(17):e170. doi: 10.1093/nar/gkq670.
