Question: Offline Tools or packages (prefer R and bioconductor packeges) for miRNA-seq time series counts data analysis of DE miRNAs ???
1
gravatar for bioinforupesh2009.au
4.9 years ago by
Spain
bioinforupesh2009.au100 wrote:

Hello all,

anyone could advise me to analyze my time series data sets of miRNA-seq ?? I have counts from HTS-seq counts after mapping. I have 4 time (T) points with 2 biological conditions (BC) and each have their replicates (r) but not equal replicates for all 2 conditions in diff time points.

for example:

    T1                          T2                          T3                           T4

BC1    BC2           BC1      BC2         BC1       BC2           BC1          BC2

_______________________________________________________________

r1          r1            r1          r1             r1         r1                 r1              r1

r2          r2            r2          r2             r2          r2                r2              r2

r3          r3             r3         r3             r3         r3                 r3             r3

r4          r4            r4          r4                                             r4             r4

r5          r5             r5                                                         r5

r6          r6

_________________________________________________________________

The above table shows my data-sets (r referred to replicates) and i dont know how to analysis and what ?? I mean, sure i would like to know DE miRNAs among them in different point. But initially i would like to see some short of preliminary analysis of my data ???

May i use 2 anova test ??? but i am not sure because, anova takes means into account and this case its not true because i have gene (miRNAs) counts. is it correct ???

Also looking forward, some R packages (bioconductor or any statistical tool, but prefer R) to detect DE miRNAs gene over time course.

 

Thank you once again for your time and waiting for kind guide line.

 

 

mirna rna-seq next-gen R • 2.6k views
ADD COMMENTlink modified 4.9 years ago by raina.kumar50 • written 4.9 years ago by bioinforupesh2009.au100
3
gravatar for raina.kumar
4.9 years ago by
raina.kumar50
United States
raina.kumar50 wrote:

You can use maSIGpro package. edgeR is also good. Looks at section 3.3 in edgeR user manual. As you have replicates you can try time course package as well.

ADD COMMENTlink written 4.9 years ago by raina.kumar50
0
gravatar for Fabio Marroni
4.9 years ago by
Fabio Marroni2.3k
Italy
Fabio Marroni2.3k wrote:

I suggest you just use R packages for RNAseq data analysis such as edgeR and DESeq. 

edgeR should also handle time series, but I am not sure because I never had time series data.

Give a read to this post: http://www.r-bloggers.com/deseq-vs-edger-comparison/

 

ADD COMMENTlink written 4.9 years ago by Fabio Marroni2.3k
1

What about maSigPro packages ??? i found it now.

http://www.ncbi.nlm.nih.gov/pubmed/24894503

ADD REPLYlink written 4.9 years ago by bioinforupesh2009.au100
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