Spanki 0.5.0 – Analysis of Alternative Splicing from RNA-Seq data

Spanki 0.5.0

:: DESCRIPTION

Spanki (Splicing Analysis Kit) is a set of tools to facilitate analysis of alternative splicing from RNA-Seq data. Spanki compiles quantitative and qualitative information about junction alignments from input BAM files, and analyzes junction-level splicing along with pairwise-defined splicing events. A simulator is also included to evaluate junction detection performance.

::DEVELOPER

The University of Maryland Center for Bioinformatics and Computational Biology (CBCB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
BioPython

:: DOWNLOAD

Spanki

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 9;14:320. doi: 10.1186/1471-2105-14-320.
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).
Sturgill D1, Malone JH, Sun X, Smith HE, Rabinow L, Samson ML, Oliver B.

TIGAR 2.1 – Estimate Transcript Isoform abundances from RNA-Seq data

TIGAR 2.1

:: DESCRIPTION

TIGAR : Transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference

::DEVELOPER

Nagasaki Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/windows/MacOsX
Java

:: DOWNLOAD

TIGAR

:: MORE INFORMATION

Citation

TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads
Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata and Masao Nagasaki
BMC Genomics, accepted (2014).

Bioinformatics. 2013 Jul 26. [Epub ahead of print]
TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.
Nariai N, Hirose O, Kojima K, Nagasaki M.

DiffSplice 0.1.2beta – Discover Alternative Splicing Variants present in an RNA-seq dataset

DiffSplice 0.1.2beta

:: DESCRIPTION

DiffSplice is a novel tool for discovering and quantitating alternative splicing variants present in an RNA-seq dataset, without relying on annotated transcriptome or pre-determined splice pattern. For two groups of samples, DiffSplice further utilizes a non-parametric permutation test to identify significant differences in expression at both gene level and transcription level. DiffSplice takes as input the SAM files that supply the alignment of the RNA-seq reads on the reference genome, obtained from an RNA-seq aligner like MapSplice. The results of DiffSplice are summarized as a decomposition of the genome and can be visualized using the UCSC genome browser.

::DEVELOPER

Bioinformatics Lab @CS.UKy.edu

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux

:: DOWNLOAD

DiffSplice

:: MORE INFORMATION

Nucleic Acids Res. 2013 Jan;41(2):e39. doi: 10.1093/nar/gks1026. Epub 2012 Nov 15.
DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J.

RNA-SeQC 1.1.8 – Quality Control Metrics for RNA-seq data

RNA-SeQC 1.1.8

:: DESCRIPTION

RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX / Windows
Java

:: DOWNLOAD

RNA-SeQC

:: MORE INFORMATION

Citation

Deluca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. (2012)
RNA-SeQC: RNA-seq metrics for quality control and process optimization.
Bioinformatics (2012) 28 (11): 1530-1532.

Rcount – Simple and Flexible RNA-Seq Read Counting

Rcount

:: DESCRIPTION

Rcount is a software for simple and flexible RNA-Seq read counting. Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA- coding genes) or to add flanking regions.

::DEVELOPER

Ueli Grossniklaus’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ WIndows/MacOsX

:: DOWNLOAD

Rcount

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 15. pii: btu680.
Rcount: simple and flexible RNA-Seq read counting.
Schmid MW, Grossniklaus U

BPSC v0.99.2 – Beta-Poisson model for single-cell RNA-seq data analyses

BPSC v0.99.2

:: DESCRIPTION

BPSC is a beta-Poisson mixture model that can capture the bimodality of the single-cell gene expression distribution. The BPSC model is into the generalized linear model (GLM) framework in order to perform differential expression analyses.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

BPSC

:: MORE INFORMATION

Citation

Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Rantalainen M, Pawitan Y.
Beta-Poisson model for single-cell RNA-seq data analyses.
Bioinformatics. 2016 Jul 15;32(14):2128-35. doi: 10.1093/bioinformatics/btw202. Epub 2016 Apr 19. PMID: 27153638.

XAEM 0.1.1 – Pipeline to Estimate Isoform Expression from RNA-seq data

XAEM 0.1.1

:: DESCRIPTION

XAEM implements the design matrix and alternating EM (AEM) algorithm, which allows a fast and accurate quantification of isoform expression using multiple samples. In differential expression (DE) analysis of single-cell data XAEM substantially outperforms other methods.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

XAEM

:: MORE INFORMATION

Citation

Deng W, Mou T, Kalari KR, Niu N, Wang L, Pawitan Y, Vu TN.
Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data.
Bioinformatics. 2020 Feb 1;36(3):805-812. doi: 10.1093/bioinformatics/btz640. PMID: 31400221.

Traph 0.7.2 – Transcript Identification and Quantification with RNA-Seq

Traph 0.7.2

:: DESCRIPTION

Traph (Transcripts in gRAPHs) is a software for RNA transcript expression prediction from RNA-sequencing data.

::DEVELOPER

GSA (Genome-scale algorithmics) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Traph

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 5:S15. doi: 10.1186/1471-2105-14-S5-S15. Epub 2013 Apr 10.
A novel min-cost flow method for estimating transcript expression with RNA-Seq.
Tomescu AI, Kuosmanen A, Rizzi R, M?kinen V.

QuASAR – Joint Genotyping & ASE Inference for RNA-seq data

QuASAR

:: DESCRIPTION

QuASAR (Quantitative allele specific analysis of reads) is an R package, that implements a statistical method for: i) genotyping from next-generation sequencing reads, and ii) conducting inference on allelic imbalance at heterozygous sites.

::DEVELOPER

Roger Pique-Regi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R

:: DOWNLOAD

QuASAR

:: MORE INFORMATION

Citation

QuASAR: Quantitative Allele Specific Analysis of Reads.
Harvey CT, Moyerbrailean GA, Davis GO, Wen X, Luca F, Pique-Regi R.
Bioinformatics. 2014 Dec 4. pii: btu802

Cufflinks 2.2.1 – Transcript Assembler & Abundance Estimator for RNA-Seq

Cufflinks 2.2.1

:: DESCRIPTION

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

::DEVELOPER

Cole Trapnell’s lab at the University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX

:: DOWNLOAD

Cufflinks

:: MORE INFORMATION

Citation

Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Nature Biotechnology doi:10.1038/nbt.1621