Scirpy v0.10.1 – Scanpy Extension for analyzing Single-cell T-cell Receptor-sequencing data

Scirpy v0.10.1

:: DESCRIPTION

Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization.

::DEVELOPER

the Institute of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Scirpy

:: MORE INFORMATION

Citation

Sturm G, Szabo T, Fotakis G, Haider M, Rieder D, Trajanoski Z, Finotello F.
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data.
Bioinformatics. 2020 Sep 15;36(18):4817-4818. doi: 10.1093/bioinformatics/btaa611. PMID: 32614448; PMCID: PMC7751015.

SKESA 2.4.0 – Strategic K-mer Extension for Scrupulous Assemblies

SKESA 2.4.0

:: DESCRIPTION

SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome.

::DEVELOPER

NCBI – National Center for Biotechnology Information

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SKESA

:: MORE INFORMATION

Citation

Souvorov A, Agarwala R.
SAUTE: sequence assembly using target enrichment.
BMC Bioinformatics. 2021 Jul 21;22(1):375. doi: 10.1186/s12859-021-04174-9. PMID: 34289805; PMCID: PMC8293564.

Souvorov A, Agarwala R, Lipman DJ.
SKESA: strategic k-mer extension for scrupulous assemblies.
Genome Biol. 2018 Oct 4;19(1):153. doi: 10.1186/s13059-018-1540-z. PMID: 30286803; PMCID: PMC6172800.

PAGAN2 20190829 – Sequence Alignment and Alignment Extension

PAGAN2 20190829

:: DESCRIPTION

PAGAN is a general-purpose method for the alignment of sequence graphs. PAGAN is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions.

::DEVELOPER

Löytynoja Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

PAGAN

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jul 1;28(13):1684-91. doi: 10.1093/bioinformatics/bts198. Epub 2012 Apr 23.
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
Löytynoja A1, Vilella AJ, Goldman N.

STAMP 1.1 – Microsatellite Marker Design Extension for the Staden package

STAMP 1.1

:: DESCRIPTION

STAMP is a Staden package extension for automating microsatellite marker design. It integrates the de novo repeat identification program Phobos by Christoph Mayer and PRIMER3 into Pregap and Gap4. It allows tagging repeats for masking them out for assembly (Pregap), finding repeats in assembled Gap4 databases, automatic primer design flanking marked repeats and multiplex primer design.

::DEVELOPER

Christoph Mayer

:: SCREENSHOTS

:: REQUIREMENTS

Linux/MacOsX / Windows
Staden

:: DOWNLOAD

STAMP

:: MORE INFORMATION

Citation

Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K. & Frickenhaus, S (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.

RNAcop 1.0.3 – Optimizing RNA structures by Sequence Extensions

RNAcop 1.0.3

:: DESCRIPTION

RNAcop (RNA Context Optimization by Probability) is a tool for optimizing lengths of flanking regions up- and downstream of a constrained structure with respect to the probability of folding into the structure.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RNAcop

:: MORE INFORMATION

Citation

Optimizing RNA structures by sequence extensions using RNAcop.
Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J.
Nucleic Acids Res. 2015 Sep 30;43(17):8135-45. doi: 10.1093/nar/gkv813.

BALBOA – Extension of Bicluster Analysis to allow for the Functional Classification of ORFs

BALBOA

:: DESCRIPTION

BALBOA is an ORF (Open Reading Frame) annotation approach, in which classifiers are constructed from the class specific expression patterns discovered by bicluster analysis. Firstly a set of bicluster classifiers is build using a labelled training set from the annotated ORFs in the expression data. These biclusters are then used to classify an unlabelled ORF set i.e. the unannotated ORFs from the expression dataset.

::DEVELOPER

the Machine Learning Group (MLG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /Mac OsX
Java

:: DOWNLOAD

BALBOA

:: MORE INFORMATION

Citation

BMC Genomics. 2008 Sep 16;9 Suppl 2:S20.
Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data.
Bryan K, Cunningham P.

GeoPhyloBuilder 1.2.1 – ArcGIS Extension that Creates Geophylogenies

GeoPhyloBuilder 1.2.1

:: DESCRIPTION

GeoPhyloBuilder is an extension for the ArcGIS geographical information system that creates a GIS network model from a tree file and sample locations

::DEVELOPER

David Kidd

:: SCREENSHOTS

:: REQUIREMENTS

Windows
ArcGIS

:: DOWNLOAD

GeoPhyloBuilder

:: MORE INFORMATION

Citation

Kidd, D. M. and M. G. Ritchie (2006).
“Phylogeographic information systems; Putting the geography into phylogeography.”
Journal of Biogeography 33: 1851-1865.

GeneFinder 1.2.7 – Linkage Analysis with a Variety of Extensions

GeneFinder 1.2.7

:: DESCRIPTION

GeneFinder is a software package for linkage analysis with a variety of extensions. GeneFinder continues a standard linkage software such as MERLIN by providing a more reasonable gene location estimation and the corresponding confidence interval estimate. In addition, GeneFinder provides a variety of linkage extensions such as adjusting for covariate heterogeneity, joint analysis of two linked disease susceptibility loci, linkage conditional on a known locus, etc.

::DEVELOPER

Wei-Min Chen

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

GeneFinder

:: MORE INFORMATION