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10xgenomics_pipeline

single cell analysis to figure out the cell type of expressed pacbio novel isoform

bigwigvis

Visualize bigWig files of RNA-seq data (supported by pyGenomeTracks)

blast_pipeline

build blast database and do blast

cdsparser

fetch CDS from genome and gff

contextdsx

test if context dependent sex-biased expression is driven by dsx

de

Differential expression analyses of RNA-seq data

demultiplexer

demultiplex bam with mixed species into specie-level sam.

dnds

A perl script to calculate dN/dS in batch based on Nei-Gojobori Method (the same as MEGA)

geouploader

upload data to geo ftp using command

interproparser

parse Gene Ontology information from interproscan output

intersectparser

calculate percentage intersected using BEDTools intersect reports

lc-practice1

lp

little piece of python script from others

ml

Use machine learning (Support Vector Machine) to predict orthologs based on sequential similarity

packaging

a notebook about how to packaging python scripts

patternrecog

pattern recognition using sklearn

pgmf

Predict Gene Model Frame

pp

Parse PicoGreen/RiboGreen results from from Gemini XPS Microplate Reader.

riborf

Identifying genome-wide translated open reading frames using ribosome profiling

simorf

The tool is meant to conduct simulation to test if an given Open Reading Frame (ORF) is significantly longer or shorter than expectation

test

test

tinypackage

toolkit

Some random tools

transana

transcript level expression analysis using Drosophila RNA-seq data by salmon and tximport

visualizebaminucsc

Visualize bam (and bigWig) in the UCSC browser