# Category Archives: Local Tools

## Calculating Pearson’s correlation coefficient in R: co-expression measure

Pearson’s correlation coefficient is a measure of the linear correlation between two variables (X and Y). The coefficient is given in a value between +1 and −1, where 1 is interpreted as total positive correlation, 0 is no correlation, and … Continue reading

## K-S goodness of fit test in Python

The Kolmogorov-Smirnov test is used to evaluate if histogram distributions deviated from a simulated null hypothesis (H0), comparing to the alternative hypothesis (H1). The distributions with P value < 0.05 are normally considered that deviated significantly from a null hypothesis. … Continue reading

## ermineJ: GO enrichment analysis

ermineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. Read more at http://erminej.chibi.ubc.ca/ Input files: GO xml file (download here); Annotation file (TAB delimited): GeneID<TAB>GeneID<TAB>Description<TAB>GO:0016020,GO:0008519… If more than one GO term is associated to a … Continue reading

## ConcaterPillar

Installation Guide of ConcaterPillar and its dependencies ConcaterPillar is a hierarchical likelihood ratio test for phylogenetic congruence. Dependences: RaxML, Python, SciPy library and pyMPI. RaxML $sudo apt-get install raxml SciPy library For linux users, just type on shell: $sudo apt-get install … Continue reading

## Bowtie 2

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its … Continue reading

## Local BLAST

“The Basic Local Alignment Search Tool (BLAST) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.” Installation for Gnome users: Website: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download $makeblastdb: Creating a local BLAST … Continue reading

## FastX Toolkit

FastX Toolkit is a collection of command line tools for short-reads file processing. Available tools FASTQ-to-FASTA converter; FASTQ Information; FASTQ/A Trimmer; FASTQ/A Reverse-Complement; FASTQ Quality Filter; Many others… Website: http://hannonlab.cshl.edu/fastx_toolkit Installation Commands: