Offline Tools or packages (prefer R and bioconductor packeges) for miRNA-seq time series counts data analysis of DE miRNAs ???

Question

[bioinforupesh2009.au]

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.

Answer 1

[raina.kumar]

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.

Answer 2

[Fabio Marroni]

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 this post a read.

[bioinforupesh2009.au]

What about maSigPro packages? I found it now.

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