[Bioc-devel] Build error for DESeq2 dev causing error in other package builds Motivation Summary graphics for RNA-sequencing and microarray gene expression analyses may contain upwards of tens of thousands of points. Details about certain genes or samples of interest are easily obscured in such de...
To run RSEM, your server should have C++, Perl and R installed. In addition, you need at least one aligner to align RNA-Seq reads for you. RSEM can call Bowtie, Bowtie 2 or STAR for you if you have them installed. Last but not least, you need to install the latest version of ...
16S rRNA-gene sequencing is a valuable approach to characterize the taxonomic content of the whole bacterial population inhabiting a metabolic and spatial niche, providing an important opportunity to study bacteria and their role in many health and envir
Sorry to disturb, the behavior of RStudio, which automatically loads packages when starting RStudio with a opening R script, may lead to serious problems when a installed package was broken. Yesterday, RStudio in my computer cannot respond to anything when I started it, likethisandthis, I tr...
We next analyzed the full and sampled datasets with DESeq, a variance-analysis package that uses a model based on the negative binomial distribution to infer statistically significant differences in gene-expression from RNA-Seq data [32]. Based on the counts of gene-mapped fragments derived from...
with a read-length of 100 bp paired-end. Resulting MT and MG reads were pre-processed with IMP28and mapped to the rMAGs reconstructed from the long-term time-series as described above. Raw read counts per CDS were determined with featureCounts74and compared with DESeq275across all ...
This collection is formed by approaches that nowadays we can call "historical", such as Total Sum Scaling, by more recent techniques, such as Cumulative Sum Scaling and the ones implemented in edgeR and DESeq2 R packages, and by a more recently developed tool, such as GMPR, that directly...
To run RSEM, your server should have C++, Perl and R installed. In addition, you need at least one aligner to align RNA-Seq reads for you. RSEM can call Bowtie, Bowtie 2 or STAR for you if you have them installed. Last but not least, you need to install the latest version of ...
When it comes to differential expression analysis, the majority of the developed software tools use external dedicated statistical packages like DESeq2 and EdgeR (iMir, miR-isomiRExp, CSB-miRSeq, sRNAtoolbox, miRpro, miRDis, Chimira, etc), or RPM normalization (DeAnniso, IsomiRage). Overall...