GitHub - slancast/Fiber

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Name	Name	Last commit message	Last commit date
Latest commit slancast Add files via upload Aug 12, 2021 8dec8b7 · Aug 12, 2021 History 3 Commits
Adding_Batch_Info.R	Adding_Batch_Info.R	Add files via upload	Aug 12, 2021
Aggreg_Clustering.R	Aggreg_Clustering.R	Add files via upload	Aug 12, 2021
Aggreg_Correlations.R	Aggreg_Correlations.R	Add files via upload	Aug 12, 2021
Baseline_means.R	Baseline_means.R	Add files via upload	Aug 12, 2021
Batch_Effects.r	Batch_Effects.r	Add files via upload	Aug 12, 2021
Batch_Effects_gf_scg.R	Batch_Effects_gf_scg.R	Add files via upload	Aug 12, 2021
Batch_Effects_rna_scg.R	Batch_Effects_rna_scg.R	Add files via upload	Aug 12, 2021
Batch_effects_gf_scg.sh	Batch_effects_gf_scg.sh	Add files via upload	Aug 12, 2021
Calculating_diversity.R	Calculating_diversity.R	Add files via upload	Aug 12, 2021
Clinical_Aggregations.R	Clinical_Aggregations.R	Add files via upload	Aug 12, 2021
Clinical_soft_clustering.R	Clinical_soft_clustering.R	Add files via upload	Aug 12, 2021
Clustering_SLedits.py	Clustering_SLedits.py	Add files via upload	Aug 12, 2021
CollectRNAseqMetrics.sh	CollectRNAseqMetrics.sh	Add files via upload	Aug 12, 2021
Concatenating_human-stool-library2.sh	Concatenating_human-stool-library2.sh	Add files via upload	Aug 12, 2021
Concatenating_second_RNA	Concatenating_second_RNA	Add files via upload	Aug 12, 2021
Concatenating_test-lib.sh	Concatenating_test-lib.sh	Add files via upload	Aug 12, 2021
DESeq2.sh	DESeq2.sh	Add files via upload	Aug 12, 2021
DESeq2_WashoutD10.r	DESeq2_WashoutD10.r	Add files via upload	Aug 12, 2021
DESeq2_condition.r	DESeq2_condition.r	Add files via upload	Aug 12, 2021
DESeq2_condition.sh	DESeq2_condition.sh	Add files via upload	Aug 12, 2021
DESeq2_fiber_week.r.sh	DESeq2_fiber_week.r.sh	Add files via upload	Aug 12, 2021
DESeq2_fiber_week_A.r	DESeq2_fiber_week_A.r	Add files via upload	Aug 12, 2021
DESeq2_fiber_week_A.sh	DESeq2_fiber_week_A.sh	Add files via upload	Aug 12, 2021
DESeq2_fiber_week_A2.R	DESeq2_fiber_week_A2.R	Add files via upload	Aug 12, 2021
DESeq2_fiber_week_B.r	DESeq2_fiber_week_B.r	Add files via upload	Aug 12, 2021
DESeq2_fiber_week_B2.R	DESeq2_fiber_week_B2.R	Add files via upload	Aug 12, 2021
DESeq2_fiber_week_submitting.txt	DESeq2_fiber_week_submitting.txt	Add files via upload	Aug 12, 2021
DESeq2_gcloud.R	DESeq2_gcloud.R	Add files via upload	Aug 12, 2021
DESeq2_gcloud_DEG.R	DESeq2_gcloud_DEG.R	Add files via upload	Aug 12, 2021
DESeq2_gcloud_baseline.R	DESeq2_gcloud_baseline.R	Add files via upload	Aug 12, 2021
DESeq2_gcloud_baseline_fall2018.R	DESeq2_gcloud_baseline_fall2018.R	Add files via upload	Aug 12, 2021
DESeq2_gcloud_baseline_old.R	DESeq2_gcloud_baseline_old.R	Add files via upload	Aug 12, 2021
DESeq2_gcloud_treatonly.R	DESeq2_gcloud_treatonly.R	Add files via upload	Aug 12, 2021
DESeq2_week.r	DESeq2_week.r	Add files via upload	Aug 12, 2021
DESeq2_week.sh	DESeq2_week.sh	Add files via upload	Aug 12, 2021
DESeq2pipe.sh	DESeq2pipe.sh	Add files via upload	Aug 12, 2021
DNAnexus.sh	DNAnexus.sh	Add files via upload	Aug 12, 2021
David.R	David.R	Add files via upload	Aug 12, 2021
David_corr_networks.R	David_corr_networks.R	Add files via upload	Aug 12, 2021
DeseqVolcanoPlot.r	DeseqVolcanoPlot.r	Add files via upload	Aug 12, 2021
EntrezID2GeneName.R	EntrezID2GeneName.R	Add files via upload	Aug 12, 2021
Gene_id.r	Gene_id.r	Add files via upload	Aug 12, 2021
GeneralizedPCLTernary.R	GeneralizedPCLTernary.R	Add files via upload	Aug 12, 2021
GeneralizedPCLTernaryMetadataLoop.R	GeneralizedPCLTernaryMetadataLoop.R	Add files via upload	Aug 12, 2021
GeneralizedRNATernary.R	GeneralizedRNATernary.R	Add files via upload	Aug 12, 2021
GeneralizedRTernary.R	GeneralizedRTernary.R	Add files via upload	Aug 12, 2021
GeneralizedRTernaryMetadataLoop.R	GeneralizedRTernaryMetadataLoop.R	Add files via upload	Aug 12, 2021
Log_normalized_data_frames.R	Log_normalized_data_frames.R	Add files via upload	Aug 12, 2021
Metagenome-C-means-clustering.R	Metagenome-C-means-clustering.R	Add files via upload	Aug 12, 2021
Metagenome-taxa-C-means-clustering.R	Metagenome-taxa-C-means-clustering.R	Add files via upload	Aug 12, 2021
MetagenomeClustering.R	MetagenomeClustering.R	Add files via upload	Aug 12, 2021
Microbiome_Clinical_Correlations.R	Microbiome_Clinical_Correlations.R	Add files via upload	Aug 12, 2021
Microbiome_Cytokine_Correlations.R	Microbiome_Cytokine_Correlations.R	Add files via upload	Aug 12, 2021
Microbiome_Cytokine_Correlations_BN.R	Microbiome_Cytokine_Correlations_BN.R	Add files via upload	Aug 12, 2021
Microbiome_Cytokine_Correlations_unBN.R	Microbiome_Cytokine_Correlations_unBN.R	Add files via upload	Aug 12, 2021
MultiomicCorrelations.R	MultiomicCorrelations.R	Add files via upload	Aug 12, 2021
Multiqc_scg.sh	Multiqc_scg.sh	Add files via upload	Aug 12, 2021
Normalize_to_baseline.r	Normalize_to_baseline.r	Add files via upload	Aug 12, 2021
Normalzied_data_frames.R	Normalzied_data_frames.R	Add files via upload	Aug 12, 2021
OmicsCorrelations.R	OmicsCorrelations.R	Add files via upload	Aug 12, 2021
PCLSupervisedClustering.R	PCLSupervisedClustering.R	Add files via upload	Aug 12, 2021
PCLTernary.R	PCLTernary.R	Add files via upload	Aug 12, 2021
Petra.1.R	Petra.1.R	Add files via upload	Aug 12, 2021
Preparing_subsets_for_responder_vs_nonresponder.R	Preparing_subsets_for_responder_vs_nonresponder.R	Add files via upload	Aug 12, 2021
RNA-C-means-clustering.R	RNA-C-means-clustering.R	Add files via upload	Aug 12, 2021
RNATernary.r	RNATernary.r	Add files via upload	Aug 12, 2021
RNA_Supervised_Clustering.R	RNA_Supervised_Clustering.R	Add files via upload	Aug 12, 2021
RNA_correlation.r	RNA_correlation.r	Add files via upload	Aug 12, 2021
RNA_from_multiomic_cmeans.R	RNA_from_multiomic_cmeans.R	Add files via upload	Aug 12, 2021
RNAfuzzy_clustering.R	RNAfuzzy_clustering.R	Add files via upload	Aug 12, 2021
RSEM4Mike	RSEM4Mike	Add files via upload	Aug 12, 2021
RSEM4Mike.sh	RSEM4Mike.sh	Add files via upload	Aug 12, 2021
RSEM_gcloud.sh	RSEM_gcloud.sh	Add files via upload	Aug 12, 2021
Responders_factor_analysis.R	Responders_factor_analysis.R	Add files via upload	Aug 12, 2021
SBA_deseq2_iterations.r	SBA_deseq2_iterations.r	Add files via upload	Aug 12, 2021
SBA_deseq2_iterations_scg.R	SBA_deseq2_iterations_scg.R	Add files via upload	Aug 12, 2021
SavingRdataFiles.R	SavingRdataFiles.R	Add files via upload	Aug 12, 2021
Saving_Data_for_Supervised.R	Saving_Data_for_Supervised.R	Add files via upload	Aug 12, 2021
SingleOmicCorrelations.R	SingleOmicCorrelations.R	Add files via upload	Aug 12, 2021
SlurmDESeqFiberWeek.sh	SlurmDESeqFiberWeek.sh	Add files via upload	Aug 12, 2021
Star.sh	Star.sh	Add files via upload	Aug 12, 2021
Subdividing_taxa.R	Subdividing_taxa.R	Add files via upload	Aug 12, 2021
Supervised_Clustering.R	Supervised_Clustering.R	Add files via upload	Aug 12, 2021
Ternary.R	Ternary.R	Add files via upload	Aug 12, 2021
TernaryPlotsOnly.R	TernaryPlotsOnly.R	Add files via upload	Aug 12, 2021
TestingVariablesDecomp.R	TestingVariablesDecomp.R	Add files via upload	Aug 12, 2021
Testing_differences_in_genefamilies.R	Testing_differences_in_genefamilies.R	Add files via upload	Aug 12, 2021
Untitled.R	Untitled.R	Add files via upload	Aug 12, 2021
Utils.r	Utils.r	Add files via upload	Aug 12, 2021
adding_master_metadata.r	adding_master_metadata.r	Add files via upload	Aug 12, 2021
bam2fastq.sh	bam2fastq.sh	Add files via upload	Aug 12, 2021
concatenating-human-stool-library-1.sh	concatenating-human-stool-library-1.sh	Add files via upload	Aug 12, 2021
concatenation.sh	concatenation.sh	Add files via upload	Aug 12, 2021
contenation.sh	contenation.sh	Add files via upload	Aug 12, 2021
create_instances.sh	create_instances.sh	Add files via upload	Aug 12, 2021
creating_samples_metadata.py	creating_samples_metadata.py	Add files via upload	Aug 12, 2021
creating_samples_metadata_renamed.py	creating_samples_metadata_renamed.py	Add files via upload	Aug 12, 2021
deseq_baseline_scg.R	deseq_baseline_scg.R	Add files via upload	Aug 12, 2021
factor_and_lda_tutorials.R	factor_and_lda_tutorials.R	Add files via upload	Aug 12, 2021
fiber_week_B.sh	fiber_week_B.sh	Add files via upload	Aug 12, 2021
fuzzy_clustering.R	fuzzy_clustering.R	Add files via upload	Aug 12, 2021
generalized_mixed_models.R	generalized_mixed_models.R	Add files via upload	Aug 12, 2021
glmer-metadata-out.R	glmer-metadata-out.R	Add files via upload	Aug 12, 2021
glmerRNAupdated11.14.R	glmerRNAupdated11.14.R	Add files via upload	Aug 12, 2021
glmer_functions.R	glmer_functions.R	Add files via upload	Aug 12, 2021
gzip_scg.sh	gzip_scg.sh	Add files via upload	Aug 12, 2021
heatmap.r	heatmap.r	Add files via upload	Aug 12, 2021
heatmap_diff_genes.R	heatmap_diff_genes.R	Add files via upload	Aug 12, 2021
immunoStates_analysis.r	immunoStates_analysis.r	Add files via upload	Aug 12, 2021
multiomic_clustering.2.R	multiomic_clustering.2.R	Add files via upload	Aug 12, 2021
multiomic_clustering.R	multiomic_clustering.R	Add files via upload	Aug 12, 2021
multiomics_correlation.r	multiomics_correlation.r	Add files via upload	Aug 12, 2021
normaggreg_multiomics_correlation.R	normaggreg_multiomics_correlation.R	Add files via upload	Aug 12, 2021
pcl-glmer-updated.R	pcl-glmer-updated.R	Add files via upload	Aug 12, 2021
pcl-updated.R	pcl-updated.R	Add files via upload	Aug 12, 2021
personalized_multiomic_clustering.R	personalized_multiomic_clustering.R	Add files via upload	Aug 12, 2021
personalized_multiomic_clustering_laptop.R	personalized_multiomic_clustering_laptop.R	Add files via upload	Aug 12, 2021
pvalue-heatmap.R	pvalue-heatmap.R	Add files via upload	Aug 12, 2021
pvalueHeatmap.R	pvalueHeatmap.R	Add files via upload	Aug 12, 2021
pvalueHistogram.R	pvalueHistogram.R	Add files via upload	Aug 12, 2021
python_FDR_RNAseq.py	python_FDR_RNAseq.py	Add files via upload	Aug 12, 2021
rename_files_from_list.sh	rename_files_from_list.sh	Add files via upload	Aug 12, 2021
responders_vs_nonresponders.R	responders_vs_nonresponders.R	Add files via upload	Aug 12, 2021
rna-targeted-decomp.r	rna-targeted-decomp.r	Add files via upload	Aug 12, 2021
rna_oct.R	rna_oct.R	Add files via upload	Aug 12, 2021
singleomic_fuzzy_clustering.R	singleomic_fuzzy_clustering.R	Add files via upload	Aug 12, 2021
submit_deseq.sh	submit_deseq.sh	Add files via upload	Aug 12, 2021
tSNE_plots.R	tSNE_plots.R	Add files via upload	Aug 12, 2021
tarballingSlurmDirectories.sh	tarballingSlurmDirectories.sh	Add files via upload	Aug 12, 2021
targeted-decomp-metaphlan-numericdose.R	targeted-decomp-metaphlan-numericdose.R	Add files via upload	Aug 12, 2021
targeted-decomp-metaphlan.R	targeted-decomp-metaphlan.R	Add files via upload	Aug 12, 2021
targeted-decomp-numericdose.R	targeted-decomp-numericdose.R	Add files via upload	Aug 12, 2021
targeted-decomp.R	targeted-decomp.R	Add files via upload	Aug 12, 2021
testing_diversity.r	testing_diversity.r	Add files via upload	Aug 12, 2021
tsne.R	tsne.R	Add files via upload	Aug 12, 2021
ttest.r	ttest.r	Add files via upload	Aug 12, 2021