kasyapgotra Goto Github PK

2021_amphistegina_rna-seq

amplicon_miseq_v4

updated version of my pipeline using the v4 primers for eukaryotic SSU

dib-mmetsp

Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)

katzlab_scripts

for working in lab

metaprot-database

These are the scripts for parsing BLASTp searches against the MetaProt database containing SEED, MMETSP, and RefSeq for annotating metagenomic and metatranscriptomic datasets. The MetaProt database (32 GB in size) of predicted proteins can be accessed and downloaded from the LMU Open Data project : https://doi.org/10.5282/ubm/data.183

micobe

microbiome

microbiome R package

phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

phylotol

r_scripts

List of scripts to work with MiSeq amplicon data

ssu_database_builiding

Here are a set of scripts I generated to built a curated SSU database, including removing redundant sequences and removing column with x% of missing characters

transcriptomics

Some scripts to download, trim and assembled transcriptomes from SRA GenBank

trinotate.github.io

web documentation for Trinotate

umassthesis

Unofficial UMass thesis style files for use with LaTeX