Name: Peer-Led-Bioinformatics
Owner: SmithsonianWorkshops
Description: Bioinformatics training series led by members of the Smithsonian community
Created: 2016-03-18 14:58:08.0
Updated: 2017-02-28 16:54:03.0
Pushed: 2017-10-27 14:58:00.0
Homepage: null
Size: 150349
Language: HTML
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|---|---|
| Mike Trizna | 2016-11-22 18:55:49.0 | 3 |
| Matthew Kweskin | 2017-10-27 14:57:59.0 | 69 |
| rdikow | 2016-04-28 15:14:41.0 | 1 |
| hawchuan | 2016-11-17 18:53:53.0 | 9 |
| gonzalezvl | 2016-04-28 18:23:17.0 | 2 |
| Mike Lloyd | 2016-11-10 18:31:03.0 | 3 |
Other Committers
| User | Most Recent Commit | # Commits | |
|---|---|---|---|
| hawchuan | big.river.forest@gmail.com | 2016-11-15 16:40:46.0 | 5 |
| Paul Frandsen | frandsenp@ocio-l32711.us.sinet.si.edu | 2016-04-05 14:57:15.0 | 3 |
| Paul Frandsen | frandsenp@ssbpc00049383.us.sinet.si.edu | 2016-03-31 17:45:56.0 | 1 |
Bioinformatics training series led by members of the Smithsonian community
Users connected to the SI Intranet can view video links here. Others, not connected to the SI network, can contact us via Github for video access.
Talks are on Thursdays from 2-3pm in WG33, Natural History Building except where noted otherwise.
Schedule is tentative and subject to change.
Date | Speaker | Topics | Packages | Session Links
—–|———|——–|———-|——————-
Thurs, Oct 13 (1pm, WG33)| Matthew Kweskin & Kenneth (Tripp) Macdonald|? R resources, R studio, Data types and concepts, packages and task views, running R on Hydra;
? Introductory R, subsetting data, exporting importing data, data classes, some statistics||Slides- Kweskin
Data files- Macdonald
Thurs, Oct 20 (2pm, WG33)| Kenneth (Tripp) Macdonald|Introductory R, subsetting data, exporting importing data, data classes, some statistics (continuation of week 1)||
Data files- Macdonald
R ref card |
Tues, Oct 25 (2pm, WG33)| Dietrich Gotzek|Assess MCMC convergence|CODA, BOA, and RWTY|
RWTY Data files
Treescape Data files
Slides
Thurs, Nov 3 (2pm, WG33) | HC Lim|Manipulating phylogenetic trees, labeling, coloring|mainly APE|
R scripts
Other data files
[Slides](Fall2016/HC-Week3/Working with trees in R.pptx)
Thurs, Nov 10 (2pm, WG33) |Michael Lloyd|Loops, files manipulations and repetitive tasks, etc||Go to this folder for materials|
Tues, Nov 15 (2pm, WG33)|Caroline Judy & Andrew Gottscho|population structure analysis|Adegenet|Go to this folder for R script and tutorial pdf|
Tues, Nov 29 (2pm, WG33)|Mike Trizna|Data wrangling|dplyr, magrittr, tidyr|Go to this folder for materials and PDF|
Thurs, Dec 1 (2pm, WG33)|Carolyn Tepolt|Plotting and data wrangling|ggplot2, data.table|Go to this folder for materials and PDF|
Thurs, Dec 8 (2pm, WG33)|Nicole Angeli|Displaying and analyzing geographic data, pattern analysis, or regression/population modeling.|phytools, spatstat, rgdal, shapefiles, rgeos, raster, and lattice|Go to this folder for materials and presentation (requires downloading html file and opening in your browser)
Thurs, Dec 15 (2pm, WG33)|Steven Calahan|Manipulating geospatial data|rgdal, ggplot2|Go to this repo
Talks are on Thursdays from 2-3pm in WG33, Natural History Building.
Date | Speaker | Topic | Links
—–|———|——|——
3/17/2016 | Andy Gottscho | PyRAD - a python pipeline for Restriction-Associated-DNA sequencing | Slides
Example on Hydra: /pool/genomics/gottschoa/test_pyrad_module
Sample param and job files
3/24/2016 | Michael Trizna | Jupyter Notebook for workflow management | Slides
Example notebook
3/31/2016 | Paul Frandsen | Data partitioning | Slides
Tutorial
4/7/2016 | Rebecca Dikow | Genome Assembly | Slides
See assembly workshop
4/14/2016 | Vanessa Gonzalez | Gene Prediction (Augustus) | Slides
4/21/2016 | Carolyn Teplot | Analysis of coexpression patterns in genes | Slides
Date | Speaker | Topic | Links —–|———|——-|——– 4/20/2015| Rebecca Dikow | Whole genome alignment/phylogeny | Slides 4/27/2015| Paul Frandsen | submitting to cluster with qsub, scripting | Hydra training site 5/4/2015| HC Lim | genotype and snp calling | Slides, GATK best practices videos (Broad) 5/11/2015| Cheryl Lewis Ames | gene prediction and annotation using Trinotate | Slides 5/18/2015| Missy Hawkins | sequence capture experiment design | Slides 6/1/2015| Matt Leray | metabarcoding data OTU calling, community-level analysis | Slides 6/8/2015| Ehsan Kayal | Phylogenomic analysis | Slides 6/15/2015| Matthew Kweskin | Tricking out your Mac: Installing analysis software on your Mac | Slides 6/22/2015| Monica C. Munoz-Torres | Web Apollo & Gene Ontology Resources for Functional Annotations | Web Apollo website 6/29/2015| Tammy Wilbert | RAD-seq library prep (pros/cons), some snp calling tools, population genomics analysis | Slides