atmaivancevic

AWS_setup

BAM

Reads and manipulates large BAM files

Clustering

Picks the best clustering % identity to use for a given organism/species, taking into account (in order of importance): (a) That higher % ids will produce better alignments (so set a minimum % threshold of 70%); (b) that each cluster needs to be 'alignable' (i.e. set the max size of any given cluster to 100 seqs; unless the % id is very high, e.g. => 90%, in which case the sequences are very similar so the max size of any cluster can be raised to, say, 500 seqs, and still produce a good alignment); (c) that we want to used the largest sample size of sequences possible (i.e. the minimum number of unclustered seqs and singletons, provided the first two conditions are satisfied).

ERV_cancer_enhancers

Gblocks

Improve alignment with gblocks to generate a better consensus

longread_vntr_analysis

Pipeline_B

Code used to detect horizontal transfer of transposons across species.

Split

structuralVariantResources

Open source tools and papers for structural variant analysis.

structuralVariants

For testing and collaborating on structural variant pipelines and best practices

atmaivancevic/structuralVariantResources

Open source tools and papers for structural variant analysis.

atmaivancevic/ERV_cancer_enhancers

atmaivancevic/Split

atmaivancevic/structuralVariants

For testing and collaborating on structural variant pipelines and best practices

atmaivancevic/AWS_setup

atmaivancevic/BAM

Reads and manipulates large BAM files

atmaivancevic/handySLURMscripts

Handy scripts to summarise job stats (memory used, elapsed time, etc) and produce summary plots

atmaivancevic/kallipygos

Single nucleotide polymorphism that gives sheep "beautiful buttocks"

atmaivancevic/longread_vntr_analysis

atmaivancevic/Pipeline_B

Code used to detect horizontal transfer of transposons across species.

atmaivancevic/2017

New Year, New me! Let's hope. This is my attempt at being an organised human being.

atmaivancevic/automated_test

testing automated pipeline for cut n run

atmaivancevic/bedtools

A powerful toolset for genome arithmetic.

atmaivancevic/beesknees

atmaivancevic/chipseq-analysis

atmaivancevic/chuonglab

General purpose scripts

atmaivancevic/cut-n-run-analysis

atmaivancevic/Elephant-project

Contains the scripts used to convert BAM to BED, generate binary sequences and infer phylogenies.

atmaivancevic/forgetfulfish

RNA-seq analysis of zebrafish models of Alzheimer's disease

atmaivancevic/genotypeGVCFs

Use a whole bunch of vcfs from the variantCalling pipeline to produce a monstrous combined gVCF

atmaivancevic/giggle_databases

Use public datasets to make giggle databases.

atmaivancevic/github_tips

How to git better

atmaivancevic/HMMer

Post-HMMer filtering of results

atmaivancevic/howToDocs

Documentation and usage examples for frequently used pipelines and tools.

atmaivancevic/L1-dynamics

Sample code to accompany the L1 evolutionary dynamics across eukaryotes manuscript. Shows how to perform two independent extraction methods: iterative search using LASTZ on genomic data, versus translated nucleotide search of NCBI databases using TBLASTN. Subsequent analyses use programs such as MUSCLE, USEARCH, HMMER, etc.

atmaivancevic/proteomics

R scripts to filter proteomics data

atmaivancevic/random-sampling

Take a random sampling of L1 and non-L1 genomic pieces

atmaivancevic/single_cell_RNAseq

atmaivancevic/Unmask

atmaivancevic/variantCalling

Testing scripts for variant calling, using human Illumina genomes/exomes