smallWig – Parallel Compression of RNA-seq WIG Files

smallWig

:: DESCRIPTION

The smallWig tool provides compression/decompression for WIG files.

::DEVELOPER

Zhiying WangTsachy (Itschak) Weissman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  smallWig

:: MORE INFORMATION

Citation

smallWig: Parallel Compression of RNA-seq WIG Files.
Wang Z, Weissman T, Milenkovic O.
Bioinformatics. 2015 Sep 30. pii: btv561.

compcodeR 1.26.1 – Benchmarking Differential Expression Methods for RNA-seq data

compcodeR 1.26.1

:: DESCRIPTION

compcodeR is an R package for comparing the results of multiple differential expression analysis methods applied to a common RNAseq data set. It also contains functionalities for simulating realistic count matrices and interfaces to several of the most widely used differential expression analysis methods for RNAseq data.

::DEVELOPER

Charlotte Soneson <Charlotte.Soneson at isb-sib.ch>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 compcodeR

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 9. [Epub ahead of print]
compcodeR – an R package for benchmarking differential expression methods for RNA-seq data.
Soneson C.

CADBURE 20151031 – Evaluating Aligner performance on your RNA-Seq dataset

CADBURE 20151031

:: DESCRIPTION

The purpose of CADBURE (Comparing Alignment results of user Data Based on the relative reliability and advantage of Uniquely aligned REads) is to evaluate spliced aligner performance on user’s RNA-Seq data by comparing a pair of alignment results obtained either from two different aligners with the similar parameter set or from two different parameter sets with the same aligner.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CADBURE

:: MORE INFORMATION

Citation

Sci Rep. 2015 Aug 25;5:13443. doi: 10.1038/srep13443.
CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data.
Kumar PK, Hoang TV, Robinson ML, Tsonis PA, Liang C

FindTail 1.01 – Accurate Detection of Poly(A)/(T) tails and other Homopolymer in RNA-Seq and ESTs

FindTail 1.01

:: DESCRIPTION

Implemented in C++, FindTail first detects all perfect poly(A) tracts (or homopolymers)in a sequence. Starting with the first tract, FindTail then determines whether the downstream tracts can be merged to form a longer poly(A) fragment using an adjustable gap. After the merging step, it calculates the identity for all resultant poly(A) fragments and remaining tracts, and filter them using an adjustable minimum identity. Finally, the poly(A) length is calculated and filtered by an adjustable minimum length.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • C++ Compiler

:: DOWNLOAD

 FindTail

:: MORE INFORMATION

eSNV-Detect v1.0 – Reliable Identification of Variants Using RNA-seq Data

eSNV-Detect v1.0

:: DESCRIPTION

The eSNV-Detect is a method to detect expressed single nucleotide variants (eSNVs) with high specificity and sensitivity from the high throughput transcriptome sequencing data. Alignments from multiple aligers are used to cover the aligner bias and multiple genomic features are used to improve the specificity. For the expressed SNVs detected, it can also identify the amino acid change and classify the protein domains.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Virtual Box
  • R package

:: DOWNLOAD

  eSNV-Detect

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Oct 28. pii: gku1005.
The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.
Tang X, Baheti S1, Shameer K, Thompson KJ, Wills Q, Niu N, Holcomb IN, Boutet SC, Ramakrishnan R, Kachergus JM, Kocher JP, Weinshilboum RM, Wang L, Thompson EA, Kalari KR

RNA-Skim – RNA-Seq Quantification at Transcript Level

RNA-Skim

:: DESCRIPTION

RNA-Skim is a rapid method for RNA-Seq quantification at transcript level

::DEVELOPER

Zhaojun Zhang , Wei Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 RNA-Skim

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i283-i292. doi: 10.1093/bioinformatics/btu288.
RNA-Skim: a rapid method for RNA-Seq quantification at transcript level.
Zhang Z, Wang W.

OneStopRNAseq – Comprehensive and Efficient analyses of RNA-seq data

OneStopRNAseq

:: DESCRIPTION

OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

Li R, Hu K, Liu H, Green MR, Zhu LJ.
OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data.
Genes (Basel). 2020 Oct 2;11(10):1165. doi: 10.3390/genes11101165. PMID: 33023248; PMCID: PMC7650687.

CRAC 2.5.2 – An Integrated RNA-Seq Read Analysis

CRAC 2.5.2

:: DESCRIPTION

CRAC is designed to find splice junctions, fusion junctions, SNVs, indels in reads. It focuses on the unique location of a read. It performs particularly well on long reads. It is designed for resequencing projects and is therefore able to map reads coming from the same species or a close one.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux

:: DOWNLOAD

 CRAC

:: MORE INFORMATION

Citation

Genome Biol. 2013 Mar 28;14(3):R30.
CRAC: an integrated approach to the analysis of RNA-seq reads.
Philippe N, Salson M, Commes T, Rivals E.

VirTect – Detection of Viruses from RNA-Seq on human samples

VirTect

:: DESCRIPTION

VirTect is a computational tool that can use to detect virus from RNA-Seq on human samples.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

VirTect

:: MORE INFORMATION

Citation

Khan A, Liu Q, Chen X, Stucky A, Sedghizadeh PP, Adelpour D, Zhang X, Wang K, Zhong JF.
Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA-seq and VirTect.
Mol Oncol. 2019 Apr;13(4):829-839. doi: 10.1002/1878-0261.12435. Epub 2019 Feb 23. PMID: 30597724; PMCID: PMC6441885.

CellR 0.1.0 – Single-cell RNA-Seq guided Deconvolution of Cellular Composition from Bulk-tissue RNA-Seq

CellR 0.1.0

:: DESCRIPTION

CellR is a single cell-based data-driven method to recover and quantify the cellular composition of bulk transcriptional data. It is a fully unsupervised approach based on clustering the reference single-cell RNA-Seq (scRNA-seq) followed by extracting the unique marker genes defining each cell cluster.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

CellR

:: MORE INFORMATION

Citation

Doostparast Torshizi A, Duan J, Wang K.
A computational tool for direct inference of cell-specific expression profiles and cellular composition from bulk-tissue RNA-seq in brain disorders.
bioRxiv, 2020.