Dr.seq statistics

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chevron_left Dimensionality reduction Normalization Quality control Read alignment UMI processing scRNA-seq data integration Clustering Drop-seq analysis Variable gene detection Transcript quantification chevron_right
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Associated diseases

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Dr.seq specifications

Information


Unique identifier OMICS_11444
Name Dr.seq
Alternative names Dr.seq2, Drseq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data The Dr.seq QC and analysis pipeline uses two paired sequencing files as input. One file contains transcript information, and the other contains cell barcode and UMI information.
Input format FASTQ or SAM/BAM
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.1.0
Stability Stable
Requirements
R
Maintained Yes

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Maintainer


  • person_outline Yong Zhang <>

Additional information


Manual: http://www.tongji.edu.cn/~zhanglab/drseq2/#Installation Previous version : http://www.tongji.edu.cn/~zhanglab/drseq/

Publications for Dr.seq

Dr.seq in publications

 (13)
PMCID: 5844153
PMID: 29540912
DOI: 10.4103/psychiatry.IndianJPsychiatry_12_18

[…] of the situation are used to score items in 4 5-item sub-scales: ‘negative affect, social/positive, physical and other concerns, and withdrawal and urges’.drink refusal self efficacy questionnaire (drseq): is a self-administered 31-item measure of drinking that measures a person's self- perceived ability to resist drinking. the questionnaire has three factors: drinking in situ ations […]

PMCID: 5762704
PMID: 29321653
DOI: 10.1038/s41598-017-18730-y

[…] dna and rna and then quantified the separated molecules. however, the profiling of the genome and transcriptome was limited to a few genes and at a low resolution. for instance, g&t-seq and dr-seq are only able to investigate the copy number variation of single cells due to loss of dna and rna during separation step, or the low efficiency of binding affinity,. techniques of revealing […]

PMCID: 5746494
PMID: 29285690
DOI: 10.1186/s40169-017-0177-y

[…] expression and dna methylation in gene body and promoter regions in neuron single cells., regarding simultaneous measurement of gene expression with another omics data generated from the same cell, dr-seq is an example of pioneering work on single-cell dna and rna parallel sequencing []. without manually separating the nucleus and cytosolic mrna, dr-seq applies a quasi-linear amplification […]

PMCID: 5591254
PMID: 28887473
DOI: 10.1038/s41598-017-10704-4

[…] within a tumour and the sensitivity for a similar analysis on circulating tumour cells (ctcs)., two recent approaches describe analysing the genome and transcriptome from the same single cell: dr-seq (gdna-mrna sequencing) and g&t-seq (genome and transcriptome sequencing). both are bench protocols with multiple handling steps, not ideal in a diagnostic setting and risking sample loss. […]

PMCID: 5477641
PMID: 28676781
DOI: 10.3389/fpsyg.2017.01025

[…] refusal self-efficacy questionnaire (grseq) (casey et al., )., both scales stemmed from previous measures of self-efficacy related to alcohol addiction: the scq-39 (annis and graham, ) and the drseq (for the gseq, see young and oei, ; for the grseq, see young et al., ). both have been developed with consideration to the broad situational classes of factors that, according to marlatt (), […]


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Dr.seq institution(s)
Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai, China
Dr.seq funding source(s)
Supported by National Natural Science Foundation of China (31571365, 31322031 and 31371288), National Key Research and Development Program of China (2016YFA0100400), Specialized Research Fund for the Doctoral Program of Higher Education (20130072110032), and Program of Shanghai Academic Research Leader (17XD1403600).

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