Tool: MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
3
gravatar for Bohdan Khomtchouk
23 months ago by
Stanford University
Bohdan Khomtchouk320 wrote:

Dear Community,

Please take a look at MicroScope: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1260-x

MicroScope is a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network visualization.

To use MicroScope, please visit: http://microscopebioinformatics.org

For developers, MicroScope source code is available at: https://github.com/Bohdan-Khomtchouk/Microscope

MicroScope is free software (released under the GNU General Public License) and you are welcome (and encouraged) to contribute to it. Please submit any bug reports here: https://github.com/Bohdan-Khomtchouk/Microscope/issues.

Please feel free to get in touch via Github, or here on Biostars.

Best regards,

Bohdan Khomtchouk

rna-seq tool chip-seq • 1.1k views
ADD COMMENTlink modified 23 months ago by genomax54k • written 23 months ago by Bohdan Khomtchouk320
1

Dear Bohdan Khomtchouk, Hi

Do you know that which one of the Trinity software pipeline can be used directly in MicroScope ?

ADD REPLYlink modified 23 months ago • written 23 months ago by Farbod3.1k

@Farbod You'll want to look at the Implementation section of the paper to see what your input into MicroScope should be: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1260-x

ADD REPLYlink written 23 months ago by Bohdan Khomtchouk320
1

Hi

The head of "Trinity_Gene_counts_.TMM.EXPR.matrix.csv " is as :

;F1;F2;F3;M1;M2;M3

TRINITY_DN2336_c0_g1;0;0.967;0.209;0;0.201;0.192

TRINITY_DN104307_c0_g1;0.354;0;0;0;1.103;0

TRINITY_DN235187_c0_g1;0;0.34;0;0;0;0

TRINITY_DN151269_c0_g1;0;0.223;0.199;0.754;0.365;0

TRINITY_DN239383_c0_g1;0.26;0.361;0.209;0.142;0.1;0

TRINITY_DN139652_c0_g1;0;0.754;0;0.426;0.155;0.155

can I use this file in microScope ?

ADD REPLYlink modified 23 months ago • written 23 months ago by Farbod3.1k

@Bohdan: Personal email addresses are not used in Biostars posts.

ADD REPLYlink written 23 months ago by genomax54k
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