TIgGER 0.4.0 – Infers Novel Immunoglobulin Alleles from Sequencing Data

TIgGER 0.4.0

:: DESCRIPTION

TIgGER (Tool for Ig Genotype Elucidation via airR-seq) is a set of methods for identifying novel V gene alleles and constructing subject-specific genotypes.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

TIgGER

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A, 112 (8), E862-70 2015 Feb 24
Automated Analysis of High-Throughput B-cell Sequencing Data Reveals a High Frequency of Novel Immunoglobulin V Gene Segment Alleles
Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH.

npSeq 1.1.1 – Significance Analysis of Sequencing data

npSeq 1.1.1

:: DESCRIPTION

npSeq is an R package for the significance analysis of sequencing data.  The statistic used by npSeq is exactly the same as that in SAM 4.0. The only difference is that npSeq uses symmetric cutoffs, while SAM uses asymmetric cutoffs. Therefore, for some datasets, all significant genes obtained by SAM are either all up-regulated or all down-regulated, but npSeq almost always gives significant genes that include both up-regulated genes and down-regulated genes.

::DEVELOPER

Jun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/  Linux / WIndows
  • R Package

:: DOWNLOAD

 npSeq

:: MORE INFORMATION

Citation

Jun Li and Robert Tibshirani (2011)
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.
Stat Methods Med Res. 2011 Nov 28.

fineSTRUCTURE 4.0.1 – Identify Population Structure using Dense Sequencing Data

fineSTRUCTURE 4.0.1

:: DESCRIPTION

fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.  By using the output of ChromoPainter as a (nearly) sufficient summary statistic, it is able to perform model-based Bayesian clustering on large datasets, including full resequencing data, and can handle up to 1000s of individuals.

::DEVELOPER

Daniel Lawson

:: SCREENSHOTS

fineSTRUCTURE

:: REQUIREMENTS

  • Linux / Windows with  MinGW/ MacOsX

:: DOWNLOAD

  fineSTRUCTURE

:: MORE INFORMATION

Citation

Lawson, Hellenthal, Myers, and Falush (2012),
Inference of population structure using dense haplotype data“,
PLoS Genetics, 8 (e1002453).

CAGEr 1.28.0 – Analysis of CAGE (Cap Analysis of Gene Expression) Sequencing Data

CAGEr 1.28.0

:: DESCRIPTION

CAGEr is an R implementation of novel methods for the analysis of differential TSS usage and promoter dynamics, integrated with CAGE data processing and promoterome mining into a first comprehensive CAGE toolbox on a common analysis platform.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 CAGEr

:: MORE INFORMATION

Citation

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.
Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B.
Nucleic Acids Res. 2015 Feb 4. pii: gkv054.

VARIFI – Variant Identification, Filtering and Annotation of Amplicon Sequencing Data

VARIFI

:: DESCRIPTION

VARIFI is a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)).

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

VARIFI-Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data.
Krunic M, Venhuizen P, Müllauer L, Kaserer B, von Haeseler A.
J Pers Med. 2019 Feb 1;9(1). pii: E10. doi: 10.3390/jpm9010010.

BitSeq 0.7.5 / for R 1.16.0 – Bayesian Inference of Transcripts from Sequencing Data

BitSeq 0.7.5 / for R 1.16.0

:: DESCRIPTION

BitSeq is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts.

:: DEVELOPER

Peter Glaus , Antti Honkela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • GCC / BioCOnductor/ R package
  • Python

:: DOWNLOAD

 BitSeq / for R

:: MORE INFORMATION

Citation

Fast and accurate approximate inference of transcript expression from RNA-seq data.
Hensman J, Papastamoulis P, Glaus P, Honkela A, Rattray M.
Bioinformatics. 2015 Aug 26. pii: btv483

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.
Identifying differentially expressed transcripts from RNA-seq data with biological variation.
Glaus P, Honkela A, Rattray M.

CircTest 0.1.0 / DCC 0.3.2 – Identification and Quantification of Circular RNAs from Sequencing Data

CircTest 0.1.0 / DCC 0.3.2

:: DESCRIPTION

CircTest tests the variation of circRNAs in respect to host genes.

DCC (detect circRNAs from chimeric reads) is a python package intended to detect and quantify circRNAs with high specificity.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R
  • Python

:: DOWNLOAD

 CircTest , DCC

:: MORE INFORMATION

Citation

Specific identification and quantification of circular RNAs from sequencing data.
Cheng J, Metge F, Dieterich C.
Bioinformatics. 2015 Nov 9. pii: btv656

Reveel – Large-scale Population Genotyper using low-coverage Sequencing data

Reveel

:: DESCRIPTION

Reveel is an ultrafast tool for single nucleotide variant calling and genotyping of large cohorts that have been sequenced at low coverage.

::DEVELOPER

Lin Huang <linhuang@cs.stanford.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 Reveel

:: MORE INFORMATION

Citation

Reveel: large-scale population genotyping using low-coverage sequencing data.
Huang L, Wang B, Chen R, Bercovici S, Batzoglou S.
Bioinformatics. 2015 Sep 9. pii: btv530.

ReportingTools 2.8.0 – Tools for Making Microarray and Sequencing Data Reports in various Formats

ReportingTools 2.8.0

:: DESCRIPTION

The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel.

:: DEVELOPER

Jason A. Hackney <hackney.jason at gene.com>, Melanie Huntley, Jessica L. Larson, Christina Chaivorapol, Gabriel Becker <gmbecker at ucdavis.edu>, and Josh Kaminker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

  ReportingTools

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 18.
ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.
Huntley MA, Larson JL, Chaivorapol C, Becker G, Lawrence M, Hackney JA, Kaminker JS.

Mutascope 1.0.2 – Analysis software designed for PCR-amplicon Sequencing data

Mutascope 1.0.2

:: DESCRIPTION

Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.

::DEVELOPER

frazer Lab, UCSD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R package
  • MCLUST
  • SAMTools
  • BWA

:: DOWNLOAD

 Mutascope

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1908-9. doi: 10.1093/bioinformatics/btt305. Epub 2013 May 27.
Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing.
Yost SE, Alakus H, Matsui H, Schwab RB, Jepsen K, Frazer KA, Harismendy O.