BCseq – Accurate Single Cell RNA-seq Quantification with Bias Correction

BCseq

:: DESCRIPTION

BCseq (bias-corrected sequencing analysis) is a software tool to quantify gene expression from scRNA-seq.

:: DEVELOPER

Liang Chen’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R

:: DOWNLOAD

BCseq

:: MORE INFORMATION

Citation:

BCseq: accurate single cell RNA-seq quantification with bias correction.
Chen L, Zheng S.
Nucleic Acids Res. 2018 Aug 21;46(14):e82. doi: 10.1093/nar/gky308.

MIRPIPE 1.2.1 – miRNA detection and quantification pipeline

MIRPIPE 1.2.1

:: DESCRIPTION

MIRPIPE enables rapid and simple browser-based miRNA homology detection and quantification.

::DEVELOPER

the Loosolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MIRPIPE

:: MORE INFORMATION

Citation:

MIRPIPE – quantification of microRNAs in niche model organisms.
Kuenne C, Preussner J, Herzog M, Braun T, Looso M.
Bioinformatics. 2014 Aug 26. pii: btu573.

MaLTA – Transcriptome Assembly and Quantification from Ion Torrent RNA-Seq data

MaLTA

:: DESCRIPTION

MaLTA is a method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data.

::DEVELOPER

Georgia State University NGS Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 MaLTA

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jul 14;15 Suppl 5:S7. doi: 10.1186/1471-2164-15-S5-S7. Epub 2014 Jul 14.
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.
Mangul S, Caciula A, Al Seesi S, Brinza D, M?ndoiu I, Zelikovsky A.

Salmon v1.0.0 – Quantification of Transcript Abundance from RNA-seq reads

Salmon v1.0.0

:: DESCRIPTION

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

Salmon

:: MORE INFORMATION

Citation

Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford (2017).
Salmon provides fast and bias-aware quantification of transcript expression.
Nature Methods 14:417-419.

QAPA 1.3.0 – RNA-seq Quantification of Alternative Polyadenylation

QAPA 1.3.0

:: DESCRIPTION

QAPA (Quantification of APA) is a method that infers APA from conventional RNA-seq data.

::DEVELOPER

Morris Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Python

:: DOWNLOAD

QAPA

:: MORE INFORMATION

Citation

Genome Biol. 2018 Mar 28;19(1):45. doi: 10.1186/s13059-018-1414-4.
QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data.
Ha KCH, Blencowe BJ, Morris Q

AbundantOTU+ 0.93b – Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA

AbundantOTU+ 0.93b

:: DESCRIPTION

AbundantOTU+ deals with sequences from rare species as well, compared to AbundantOTU!!

AbundantOTU is a software based on a Consensus Alignment (CA) algorithm,which infers consensus sequences, each representing an OTU,taking advantage of the sequence redundancy for abundant species. Pyrosequencing reads can then be recruited to the consensus sequences to give quantitative information for the corresponding species. As tested on 16S rRNA pyrosequence datasets from mock communities with known species, AbundantOTU rapidly reported identiffied sequences of the source 16S rRNAs and the abundances of the corresponding species.AbundantOTU was also applied to 16S rRNA pyrosequence datasets derived from real microbial communities and the results are in general agreement with previous studies.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 AbundantOTU+

:: MORE INFORMATION

Citation:

Yuzhen Ye.
Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment.
The Proceedings of BIBM 2010, 153-157

Net-RSTQ – Network-based method for RNA-Seq-based Transcript Quantification

Net-RSTQ

:: DESCRIPTION

Net-RSTQ is a software to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation.

::DEVELOPER

KUANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 Net-RSTQ

:: MORE INFORMATION

Citation

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.
Zhang W, Chang JW, Lin L, Minn K, Wu B, Chien J, Yong J, Zheng H, Kuang R.
PLoS Comput Biol. 2015 Dec 23;11(12):e1004465. doi: 10.1371/journal.pcbi.1004465.

StringTie 2.0.3 – Transcript Assembly and Quantification for RNA-Seq

StringTie 2.0.3

:: DESCRIPTION

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 StringTie

:: MORE INFORMATION

Citation

Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18.
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL

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

FT-ARM – Identification and Quantification of Multiplexed High-resolution

FT-ARM

:: DESCRIPTION

FT-ARM (Fourier transform-all reaction monitoring) is a software package which allows you to search and quantify peptides from data acquired in a multiplexed acquisition scheme. This data is typically acquired over some defined mass window during the entire chromatogram (ex. 700-800 m/z). Presently this software supports Thermo .raw files from any high resolution platform (ex. LTQ-FT, Orbitrap). However, we plan to extend support to all instrument vendors via the Proteowizard library.

::DEVELOPER

The Bruce Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 FT-ARM

:: MORE INFORMATION

Citation

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification.
Weisbrod CR, Eng JK, Hoopmann MR, Baker T, Bruce JE.
J. Proteome Res., 2012, 11 (3), pp 1621–1632