ISP 0.3
:: DESCRIPTION
ISP is a software for accurate inference of isoforms from multiple sample RNA-Seq Data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- C++ Compiler
:: DOWNLOAD
:: MORE INFORMATION
Tag: Isoform
IsoInfer 0.9.1 – Inference of Isoforms from Short Sequence Reads
IsoInfer 0.9.1
:: DESCRIPTION
IsoInfer is a program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- C/C++ Compiler
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Comput Biol. 2011 Mar;18(3):305-21. doi: 10.1089/cmb.2010.0243.
Inference of isoforms from short sequence reads.
Feng J1, Li W, Jiang T.
TITINdb – Database of Titin Structure, Sequence, Isoform, Variant and Disease Information
TITINdb
:: DESCRIPTION
TITINdb is a web application which integrates titin structure, sequence, isoform, variant and disease information.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Web browser
:: DOWNLOAD
:: MORE INFORMATION
Citation
Laddach A, Gautel M, Fraternali F.
TITINdb-a computational tool to assess titin’s role as a disease gene.
Bioinformatics. 2017 Nov 1;33(21):3482-3485. doi: 10.1093/bioinformatics/btx424. PMID: 29077808; PMCID: PMC5860166.
FlipFlop 1.8.0 – Fast Lasso-based Isoform Prediction as a Flow Problem
FlipFlop 1.8.0
:: DESCRIPTION
FlipFlop is a fast method for de novo transcript discovery and abundance estimation from RNA-Seq data.
::DEVELOPER
Centre for Computational Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows/Linux/MacOsX
- R package
- BioConductor
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 May 9.
Efficient RNA Isoform Identification and Quantification from RNA-Seq Data with Network Flows.
Bernard E, Jacob L, Mairal J, Vert JP.
Ballgown – Isoform-level Differential Expression Analysis in R
Ballgown
:: DESCRIPTION
Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly.
::DEVELOPER
The Center for Computational Biology at Johns Hopkins University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Mac OsX
- R/BioCouductor
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Biotechnol. 2015 Mar;33(3):243-6. doi: 10.1038/nbt.3172.
Ballgown bridges the gap between transcriptome assembly and expression analysis.
Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT
LIQA – Long-read Isoform Quantification and Analysis
LIQA
:: DESCRIPTION
LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data. LIQA incorporates base-pair quality score and isoform-specific read length information to assign different weights across reads instead of summarizing isoform-specific read counts directly. Moreover, LIQA can detect DAS events between conditions using isoform usage estimates.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- Pyton
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yu Hu, Li Fang, Xuelian Chen, Jiang F. Zhong, Mingyao Li, Kai Wang.
LIQA: Long-read Isoform Quantification and Analysis.
2020. bioRxiv doi: https://doi.org/10.1101/2020.09.09.289793
WemIQ – Isoform Quantification method for RNA-seq data
WemIQ
:: DESCRIPTION
WemIQ is a software tool to quantify isoform expression and exon splicing ratios from RNA-seq data accurately and robustly.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
:: DOWNLOAD
:: MORE INFORMATION
Citation
WemIQ: An accurate and robust isoform quantification method for RNA-seq data.
Zhang J, Kuo CC, Chen L.
Bioinformatics. 2014 Nov 17. pii: btu757.
IsoEM 2.0.0 – Inferring Alternative Splicing Isoform Frequencies from High-Throughput RNA-Seq Data
IsoEM 2.0.0
:: DESCRIPTION
IsoEM package can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. IsoEM uses a novel expectation-maximization algorithm that exploits read disambiguation information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand, and read pairing information (if available). Empirical experiments on synthetic datasets show that the algorithm significantly outperforms existing methods of isoform and gene expression level estimation from RNA-Seq data
::DEVELOPER
Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
- Windows / Linux / Mac OsX
- Java
:: DOWNLOAD
:: MORE INFORMATION
Citation:
M. Nicolae and S. Mangul and I.I. Mandoiu and A. Zelikovsky,
Estimation of alternative splicing isoform frequencies from RNA-Seq data,
Algorithms for Molecular Biology , pp. to appear, 2011
Ribomap v1.2 – Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abudance
Ribomap v1.2
:: DESCRIPTION
Ribomap is a package that generates isoform-level ribosome profiles from ribosome profiling data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / MacOs
- Sailfish/Salmon
:: DOWNLOAD
:: MORE INFORMATION
Citation
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Wang H, McManus J, Kingsford C.
Bioinformatics. 2016 Jun 15;32(12):1880-2. doi: 10.1093/bioinformatics/btw085
MetaPred – Prediction of Cytochrome P450 Isoform responsible for Metabolizing a Drug Molecule
MetaPred
:: DESCRIPTION
MetaPred Server predict metabolizing CYP isoform of a drug molecule/substrate, based on SVM models developed using CDK descriptors.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Web Browser
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Pharmacol. 2010 Jul 16;10:8. doi: 10.1186/1471-2210-10-8.
Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule.
Mishra NK1, Agarwal S, Raghava GP.