STREAM v1.0 – Trajectory analysis from Single-cell RNAseq and ATACseq data

STREAM v1.0

:: DESCRIPTION

STREAM (Single-cell Trajectories Reconstruction, Exploration And Mapping) is an interactive computational pipeline for reconstructing complex celluar developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

STREAM

:: MORE INFORMATION

Citation

Nat Commun, 10 (1), 1903 2019 Apr 23
Single-cell Trajectories Reconstruction, Exploration and Mapping of Omics Data With STREAM
Huidong Chen, et al.

pulseR 1.0.3 – Analysis of RNA Metabolic Kinetics from RNAseq data

pulseR 1.0.3

:: DESCRIPTION

pulseR is an R package which aims to handle such count data derived from the pulse-chase RNAseq experiments.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

pulseR 

:: MORE INFORMATION

Citation

Uvarovskii A, Dieterich C.
pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments.
Bioinformatics. 2017 Oct 15;33(20):3305-3307. doi: 10.1093/bioinformatics/btx368. PMID: 29028260.

RNASeqBrowser V3.1 – A Genome Browser for Strand Specific RNAseq Reads

RNASeqBrowser V3.1

:: DESCRIPTION

RNASeqBrowser is a visualization tool that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks — all being dynamically built from the BAM file.

::DEVELOPER

RNASeqBrowser team

:: SCREENSHOTS

RNASeqBrowser

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

  RNASeqBrowser

:: MORE INFORMATION

PROPER 1.24.0 – PROspective Power Evaluation for RNAseq

PROPER 1.24.0

:: DESCRIPTION

PROPER is an R package for power assessment and sample size determination for RNA-seq.

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R

:: DOWNLOAD

   PROPER

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jan 15;31(2):233-41. doi: 10.1093/bioinformatics/btu640.
PROPER: comprehensive power evaluation for differential expression using RNA-seq.
Wu H1, Wang C1, Wu Z

tweeDEseq 1.30.0 – Analyzing RNAseq Count data

tweeDEseq 1.30.0

:: DESCRIPTION

tweeDEseq is an R package for analyzing RNAseq count data. It implements Poisson-Tweedie family of distributions to model count data distribution. This family includes Poisson and Negative Bionomial as particular cases. The testPT test is used to detect genes that are differentially expressed (DE).

::DEVELOPER

Bioinformatic Research Group in Epidemiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 tweeDEseq

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 21;14:254. doi: 10.1186/1471-2105-14-254.
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.
Esnaola M1, Puig P, Gonzalez D, Castelo R, Gonzalez JR.