GitHub - Robert-Lewis-NZ/Rarotonga_2019_shaded_vs_exposed: Bioinformatics, photobiology, data and statistical analyses, figure generation

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Bioinformatics, photobiology, data and statistical analyses, figure generation

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Name		Name	Last commit message	Last commit date
Latest commit History 8 Commits
HC00140756_psba_reseq		HC00140756_psba_reseq
PAM_data		PAM_data
ocean_optics_data		ocean_optics_data
.RData		.RData
.Rhistory		.Rhistory
C3_C1_psba_tree_w_alignment.ai		C3_C1_psba_tree_w_alignment.ai
ETRparams.rds		ETRparams.rds
ETRparams_no_PAR_adjust.RDS		ETRparams_no_PAR_adjust.RDS
FqFmparams_no_PAR_adjust.rds		FqFmparams_no_PAR_adjust.rds
ITS2_kmer.tree		ITS2_kmer.tree
ITS2_kmer_rare.tree		ITS2_kmer_rare.tree
NMDS_df.RDS		NMDS_df.RDS
Nitschke_et_al_Symbiodiniaceae_distances.csv		Nitschke_et_al_Symbiodiniaceae_distances.csv
Nitschke_et_al_distances_key.csv		Nitschke_et_al_distances_key.csv
PAM.RDS		PAM.RDS
PSBA_metadata		PSBA_metadata
RAxML_C1_result.result		RAxML_C1_result.result
RAxML_C3_result.result		RAxML_C3_result.result
Rarotonga_ITS2.Rmd		Rarotonga_ITS2.Rmd
Rarotonga_cve_Sanger_psbA.Rmd		Rarotonga_cve_Sanger_psbA.Rmd
Rorotonga_cve_photobiology.Rmd		Rorotonga_cve_photobiology.Rmd
aligned.fasta		aligned.fasta
aligned_C1_fwd.fasta		aligned_C1_fwd.fasta
aligned_C1_fwd_manual.fasta		aligned_C1_fwd_manual.fasta
aligned_C1_rev.fasta		aligned_C1_rev.fasta
aligned_C3_fwd.fasta		aligned_C3_fwd.fasta
aligned_C3_rev.fasta		aligned_C3_rev.fasta
differential_ASV.rds		differential_ASV.rds
differential_MED.rds		differential_MED.rds
differential_abundance.rds		differential_abundance.rds
differential_abundance_MED.rds		differential_abundance_MED.rds
dynamQ_max_EnormEk.rds		dynamQ_max_EnormEk.rds
envfit_res.RDS		envfit_res.RDS
fwd_rev_c1_aligned_trimmed.fasta		fwd_rev_c1_aligned_trimmed.fasta
fwd_rev_c3_aligned_trimmed.fasta		fwd_rev_c3_aligned_trimmed.fasta
help.R		help.R
long_fwd_rev_C1.rds		long_fwd_rev_C1.rds
long_fwd_rev_C3.rds		long_fwd_rev_C3.rds
melt.RDS		melt.RDS
melt_4_deseq2.RDS		melt_4_deseq2.RDS
metadata_complete.csv		metadata_complete.csv
onemC_max_EnormEk.rds		onemC_max_EnormEk.rds
onemQ_max_EnormEk.rds		onemQ_max_EnormEk.rds
pair_wise_photo.RDS		pair_wise_photo.RDS
pair_wise_photo_Ek_FqFmmax.RDS		pair_wise_photo_Ek_FqFmmax.RDS
phyloseq_data.rds		phyloseq_data.rds
post_MED_abs.RDS		post_MED_abs.RDS
post_MED_hydno3d_abs.RDS		post_MED_hydno3d_abs.RDS
post_MED_seqs.absolute.abund_and_meta.txt		post_MED_seqs.absolute.abund_and_meta.txt
post_MED_seqs.absolute.abund_only.txt		post_MED_seqs.absolute.abund_only.txt
profiles.absolute.abund_and_meta.txt		profiles.absolute.abund_and_meta.txt
profiles.relative.abund_and_meta.txt		profiles.relative.abund_and_meta.txt
ps.RDS		ps.RDS
ps_rare_w_kmer_tree.rds		ps_rare_w_kmer_tree.rds
ps_sub_w_kmer_tree.rds		ps_sub_w_kmer_tree.rds
rdb.rds		rdb.rds
scores.RDS		scores.RDS
seqtab.nochim.rds		seqtab.nochim.rds
seqtab.nochim.tax.rds		seqtab.nochim.tax.rds
seqtab.nochim.tax_bs.rds		seqtab.nochim.tax_bs.rds
seqtab.rds		seqtab.rds
tdb.rds		tdb.rds
total_brightness.rds		total_brightness.rds