CITE-sort – Artificial-cell-type Aware Surface Marker Clustering method for CITE-seq data

CITE-sort

:: DESCRIPTION

CITE-sort conducts auto-gating with CITE-seq ADT data using recursive Gaussian Mixture Model. It is robust against artificial cell types that stem from multiplets. CITE-sort also provides concrete explanations of its internal decision process by constructing a biologically meaningful sort tree.

::DEVELOPER

Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

CITE-sort

:: MORE INFORMATION

Citation

Lian Q, Xin H, Ma J, Konnikova L, Chen W, Gu J, Chen K.
Artificial-cell-type aware cell-type classification in CITE-seq.
Bioinformatics. 2020 Jul 1;36(Suppl_1):i542-i550. doi: 10.1093/bioinformatics/btaa467. PMID: 32657383; PMCID: PMC7355304.

PAIRPred 1.0 – Partner Aware Interacting Residue PREDictor

PAIRPred 1.0

:: DESCRIPTION

PAIRPred is a partner specific protein-protein interaction site predictor that can make accurate predictions of whether a pair of residues from two different proteins interact or not.

::DEVELOPER

PAIRPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

PAIRPred

:: MORE INFORMATION

Citation

PAIRpred: partner-specific prediction of interacting residues from sequence and structure.
Minhas Fu, Geiss BJ, Ben-Hur A.
Proteins. 2014 Jul;82(7):1142-55. doi: 10.1002/prot.24479.

CASPER 0.8.2 – Context-Aware Scheme for Paired-End Read

CASPER 0.8.2

:: DESCRIPTION

CASPER is a state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.

::DEVELOPER

Data Science Laboratory, Seoul National University.

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux

:: DOWNLOAD

CASPER

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 9:S10. doi: 10.1186/1471-2105-15-S9-S10. Epub 2014 Sep 10.
CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing.
Kwon S, Lee B, Yoon S.

SVEngine – Allele Specific and Haplotype Aware Structural Variants Simulator

SVEngine

:: DESCRIPTION

SVEngine (Structural Variants Engine) is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Python

:: DOWNLOAD

SVEngine

:: MORE INFORMATION

Citation

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy081.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.
Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP

HAXAT 1.04 – Homopolymer Aware Cross Alignment Tool

HAXAT 1.04

:: DESCRIPTION

HAXAT uses a novel dynamic programming algorithm for solving the optimal local alignment between a 454 nucleotide and a protein sequence by allowing frame-shifts, guided by 454 flowpeak values.

::DEVELOPER

IFM Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

HAXAT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 12;13:230. doi: 10.1186/1471-2105-13-230.
Highly improved homopolymer aware nucleotide-protein alignments with 454 data.
Lysholm F.