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

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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

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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

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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

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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

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Local BLAST

BLAST is certainly the most widely used (and cited!) sequence similarity search tool. It can be applied to a massive variety of purposes such as gene annotation, search for orthologs and paralogs, phylogenetic inferences… Web BLAST:https://blast.ncbi.nlm.nih.gov/Blast.cgi The program compares nucleotide … Continue reading

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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:

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