Pinned Repositories
bayesSpatioTemp
We're going to work slowly through Wikle, Zammit-Mangion, and Cressie's Spatio-Temporal Statistics with R (2019), using as much python and d3js as possible. Should only take 5 years or so.
bitty_meadow_mycena_analysis
BPwebsite
cavePseudogymnoascus
coffeeResearch
Texts and graphics for proprosal for a possible reasearch project on La Roya in Cotacachi canton
Ecuador_GIS
FA_ABM
Trying to use MESA to create an agent-based model of the Foraging Ascomycete Hypothesis
fichtelgebirgeSoils
Bioinformatic processing of reads from an illumina miseq run, from soil samples.
franzITSreads
Let's run's Franz's ITS reads through a dada2 pipeline.
mimulusSpeckling
My code additions to Arielle Cooley and Doug Hundley's petal image analysis project. Python/Matlab
danchurch's Repositories
danchurch/Ecuador_GIS
danchurch/FA_ABM
Trying to use MESA to create an agent-based model of the Foraging Ascomycete Hypothesis
danchurch/fichtelgebirgeSoils
Bioinformatic processing of reads from an illumina miseq run, from soil samples.
danchurch/mimulusSpeckling
My code additions to Arielle Cooley and Doug Hundley's petal image analysis project. Python/Matlab
danchurch/bayesSpatioTemp
We're going to work slowly through Wikle, Zammit-Mangion, and Cressie's Spatio-Temporal Statistics with R (2019), using as much python and d3js as possible. Should only take 5 years or so.
danchurch/bitty_meadow_mycena_analysis
danchurch/BPwebsite
danchurch/cavePseudogymnoascus
danchurch/coffeeResearch
Texts and graphics for proprosal for a possible reasearch project on La Roya in Cotacachi canton
danchurch/franzITSreads
Let's run's Franz's ITS reads through a dada2 pipeline.
danchurch/FunctionalMicrobiomePractical
Here we will keep the scripts that we generate, as we learn about the BASH terminal for metabarcoding and metagenomic pipelines.
danchurch/geneClusterSurveyIdeas
Some ideas for methods and primers for conducting low-cost surveys for microbiome gene clusters across BCI
danchurch/getConcsFromUrl
danchurch/grass-endophyte-community
danchurch/interactiveImbaburaMiningMap
this is a toy map of the 2018 mining concessions that have been awarded for the Imbabura province of Ecuador. This is mostly an educational exercise in mapping with d3js v6 for me.
danchurch/losCedrosTrees
Let's look at the several tree data sets available for los Cedros and see what we can do with them.
danchurch/MimulusLuteus_RNAseq
danchurch/Mna_mapScaffold26
Look for a region of interest in the Mimulus naiandinus unassembled genome
danchurch/MnaXlut_genome
danchurch/nanopore_mockcommunity
danchurch/nanoporeBasics
These are the scripts for some of our first explorations with Nanopore data at the Ecological Microbiology department of UniBayreuth.
danchurch/nanoporeHostDepletionSpruce
Playing with Nanopore adaptive sampling capabilities, to see if we can directly sequence spruce microbiomes.
danchurch/nanoporeNostoc16sAlignments
untangling the results of a hail-mary 16s sequencing on a Nostoc colony PCR
danchurch/PRFB2018app
grant app and bioinformatic scripts for dealing with the preliminary data (RNAseq from doug fir)
danchurch/sphagnumCUEmetabarcoding
Scripts for the sampling of sphagnum CUE project with Bodenoekologie
danchurch/taiwan_combined_biom
This is our pipeline for building a common biom table that includes all three sequencing efforts from our study in taiwan in 2013. Authors Dan Thomas and Roo Vandegrift.
danchurch/taiwan_combined_stats
danchurch/taiwan_dada2
Here we'll give dada2 a swing, see if we repeat our results from the 2016 uparse pipeline of the taiwan reads.
danchurch/taiwan_eco_revision
danchurch/ZheStreamData
Let's poke at the gene abundance matrices and MAGs from Zhe Wang's data