Tool:MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
0
3
Entering edit mode
7.8 years ago

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 ChIP-Seq • 3.0k views
ADD COMMENT
1
Entering edit mode

Dear Bohdan Khomtchouk, Hi

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

ADD REPLY
0
Entering edit mode

@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 REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1697 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6