ConYel/wind-version1.0.1.zip
ConYel-wind-83b1b90
.gitignore
40 Bytes
Datasets_analysis
GSE68246
DEA_Breast_Cancer_CSC_GRCh38_08_Mar_2021
GSE68246_spheroid_vs_mono_heatmap_FC_18_Mar_2021.tiff.gz
546.5 kB
Public_results_GSE68246.xlsx
206.8 kB
all_comp_voom_QW_DE_targets_predicted_08_Mar_2021.txt
21.9 kB
all_comparisons_voom_QW_TMM_salmon_fc_LFCs_08_Mar_2021.txt
228.0 kB
all_logFC_voom_QW_DE_piRNA_08_Mar_2021.txt
3.4 kB
all_logFC_voom_QW_DE_piRNA_18_Mar_2021.txt
3.4 kB
featureCounts
DE_fc_edgR_TMMSpheroid_Mono.txt
203.5 kB
DE_fc_vm_QW_TMM_Spheroid_Mono.txt
290.2 kB
hist_edger_p_value_Spheroid_Mono.pdf
4.8 kB
hist_limma_p_value_Spheroid_Mono.pdf
4.8 kB
public_and_all_comp_voom_QW_TMM_salmon_fc_LFCs_08_Mar_2021.txt
346.8 kB
salmon
DE_salmon_edgR_TMM_Spheroid_Mono.txt
109.8 kB
DE_salmon_vm_QW_TMM_Spheroid_Mono.txt
156.3 kB
hist_edger_p_value_Spheroid_Mono.pdf
4.7 kB
hist_limma_p_value_Spheroid_Mono.pdf
4.8 kB
venn_diagram_DE_salmon_fC_edgeR.pdf
8.0 kB
venn_diagram_DE_salmon_fC_limma_Spheroid_Mono.pdf
8.0 kB
EDA_Breast_Cancer_CSC_GRCh38_26_Feb_2021
featureCounts
MDS_plot_featureCounts.pdf
8.0 kB
NOISeq_biodetection_26_Feb_2021_featureCounts.pdf
22.7 kB
NOISeq_countsbio_26_Feb_2021_featureCounts.pdf
127.6 kB
PCA_plot_TMM_featureCounts.pdf
5.4 kB
RLE_plots_featureCounts.pdf
17.2 kB
annotation_fc.txt
7.8 MB
dgl_Prop_filt_featureCounts.rds
1.8 kB
dgl_cpm_filt_featureCounts.rds
1.8 kB
dgl_edger_filt_batch_featureCounts.rds
154.2 kB
dgl_edger_filt_nobatch_featureCounts.rds
145.7 kB
distance_matrix_hclust_featureCounts.pdf
37.3 kB
filtering_info_featureCounts.txt
285 Bytes
hierarchic_clust_featureCounts.pdf
30.8 kB
histogram_plot_26_Feb_2021_featureCounts.pdf
5.5 kB
list_norm_dgls_featureCounts.rds
1.9 MB
norm_cpm_RLE_featureCounts.txt
223.9 kB
norm_cpm_TMM_featureCounts.txt
224.0 kB
norm_cpm_TMMwsp_featureCounts.txt
224.1 kB
raw_reads_fc.txt
1.9 MB
stats_fc.txt
648 Bytes
voom_plots_featureCounts.pdf
244.8 kB
voom_quality_weights_plots_featureCounts.pdf
243.9 kB
length_histogram.pdf
28.4 kB
piRNA_logos_FC_salmon.pdf
100.5 kB
salmon
MDS_plot_salmon.pdf
7.8 kB
NOISeq_biodetection_26_Feb_2021_salmon.pdf
21.6 kB
NOISeq_countsbio_26_Feb_2021_salmon.pdf
35.0 kB
PCA_plot_TMM_salmon.pdf
5.3 kB
RLE_plots_salmon.pdf
17.4 kB
dgl_Prop_filt_salmon.rds
1.9 kB
dgl_cpm_filt_salmon.rds
1.9 kB
dgl_edgeR_salmon.rds
7.2 MB
dgl_edger_filt_batch_salmon.rds
175.3 kB
dgl_edger_filt_nobatch_salmon.rds
157.7 kB
distance_matrix_hclust_salmon.pdf
37.3 kB
filtering_info_salmon.txt
279 Bytes
hierarchic_clust_salmon.pdf
30.3 kB
histogram_plot_26_Feb_2021_salmon.pdf
5.4 kB
list_norm_dgls_salmon.rds
1.3 MB
norm_cpm_RLE_salmon.txt
118.0 kB
norm_cpm_TMM_salmon.txt
118.0 kB
norm_cpm_TMMwsp_salmon.txt
118.0 kB
voom_plots_salmon.pdf
150.8 kB
voom_quality_weights_plots_salmon.pdf
149.4 kB
salmon_FC_cpm_union_grouped.txt
431.5 kB
salmon_FC_cpm_union_top100.txt
21.2 kB
stats_gene_types_ids.txt
344 Bytes
GRCh38_STEP_2_prep_and_quantification_GSE68246.Rmd
7.9 kB
GRCh38_STEP_3_Exploratory_Data_Analysis_GSE68246.Rmd
24.1 kB
GRCh38_STEP_3_differential_expression_analysis_GSE68246.Rmd
15.4 kB
TCGA_BRCA
DEA_Breast_Cancer_TCGA_GRCh38_08_Mar_2021
BRCA_TCGA_tumour_vs_normal_heatmap_FC.tiff.gz
290.9 kB
all_comp_voom_QW_DE_targets_predicted_08_Mar_2021.txt
14.3 kB
all_comparisons_voom_QW_TMM_salmon_fc_LFCs_08_Mar_2021.txt
249.5 kB
featureCounts
DE_fc_edgR_TMMTumour_Normal.txt
221.5 kB
DE_fc_vm_QW_TMM_Tumour_Normal.txt
314.2 kB
hist_edger_p_value_Tumour_Normal.pdf
4.7 kB
hist_limma_p_value_Tumour_Normal.pdf
4.8 kB
salmon
DE_salmon_edgR_TMM_Tumour_Normal.txt
126.4 kB
DE_salmon_vm_QW_TMM_Tumour_Normal.txt
179.6 kB
hist_edger_p_value_Tumour_Normal.pdf
4.7 kB
hist_limma_p_value_Tumour_Normal.pdf
4.8 kB
venn_diagram_DE_salmon_fC_edgeR_Tumour_Normal.pdf
8.0 kB
venn_diagram_DE_salmon_fC_limma_Tumour_Normal.pdf
8.0 kB
EDA_Breast_Cancer_TCGA_GRCh38_04_Mar_2021
featureCounts
MDS_plot_featureCounts.pdf
9.0 kB
NOISeq_biodetection_04_Mar_2021_featureCounts.pdf
61.5 kB
NOISeq_countsbio_04_Mar_2021_featureCounts.pdf
619.5 kB
PCA_plot_TMM_featureCounts.pdf
6.4 kB
RLE_plots_featureCounts.pdf
30.7 kB
annotation_fc.txt
7.8 MB
dgl_Prop_filt_featureCounts.rds
6.2 kB
dgl_cpm_filt_featureCounts.rds
6.2 kB
dgl_edger_filt_batch_featureCounts.rds
467.4 kB
dgl_edger_filt_nobatch_featureCounts.rds
313.7 kB
distance_matrix_hclust_featureCounts.pdf
64.4 kB
filtering_info_featureCounts.txt
285 Bytes
hierarchic_clust_featureCounts.pdf
47.2 kB
histogram_plot_04_Mar_2021_featureCounts.pdf
5.5 kB
list_norm_dgls_featureCounts.rds
4.5 MB
norm_cpm_RLE_featureCounts.txt
589.9 kB
norm_cpm_TMM_featureCounts.txt
590.2 kB
norm_cpm_TMMwsp_featureCounts.txt
590.0 kB
raw_reads_fc.txt
3.1 MB
stats_fc.txt
1.6 kB
voom_plots_featureCounts.pdf
270.1 kB
voom_quality_weights_plots_featureCounts.pdf
265.8 kB
length_histogram.pdf
28.1 kB
piRNA_logos_FC_salmon.pdf
100.8 kB
salmon
MDS_plot_salmon.pdf
9.1 kB
NOISeq_biodetection_04_Mar_2021_salmon.pdf
59.0 kB
NOISeq_countsbio_04_Mar_2021_salmon.pdf
516.6 kB
PCA_plot_TMM_salmon.pdf
6.4 kB
RLE_plots_salmon.pdf
30.9 kB
dgl_Prop_filt_salmon.rds
6.8 kB
dgl_cpm_filt_salmon.rds
6.8 kB
dgl_edgeR_salmon.rds
14.8 MB
dgl_edger_filt_batch_salmon.rds
601.1 kB
dgl_edger_filt_nobatch_salmon.rds
358.4 kB
distance_matrix_hclust_salmon.pdf
63.8 kB
filtering_info_salmon.txt
281 Bytes
hierarchic_clust_salmon.pdf
46.6 kB
histogram_plot_04_Mar_2021_salmon.pdf
5.4 kB
list_norm_dgls_salmon.rds
3.3 MB
norm_cpm_RLE_salmon.txt
326.7 kB
norm_cpm_TMM_salmon.txt
326.7 kB
norm_cpm_TMMwsp_salmon.txt
326.7 kB
voom_plots_salmon.pdf
170.9 kB
voom_quality_weights_plots_salmon.pdf
170.0 kB
salmon_FC_cpm_union_grouped.txt
471.8 kB
salmon_FC_cpm_union_top100.txt
54.4 kB
stats_gene_types_ids.txt
321 Bytes
GRCh38_STEP_2_Prep_and_Quantification_TCGA_BRCA.Rmd
9.4 kB
GRCh38_STEP_3_Differential_Expression_Analysis_TCGA_BRCA.Rmd
13.5 kB
GRCh38_STEP_3_Exploratory_Data_Analysis_TCGA_BRCA.Rmd
23.5 kB
Testis_COLO205
EDA_spike_ins_COLO205_Testis_GRCh38_25_Feb_2021
featureCounts
NOISeq_biodetection_25_Feb_2021_featureCounts.pdf
52.8 kB
NOISeq_countsbio_25_Feb_2021_featureCounts.pdf
607.0 kB
RLE_plots_featureCounts.pdf
24.3 kB
annotation_fc.txt
7.8 MB
dgl_Prop_filt_featureCounts.rds
3.3 kB
dgl_cpm_filt_featureCounts.rds
3.3 kB
dgl_edger_filt_batch_featureCounts.rds
2.8 MB
dgl_edger_filt_nobatch_featureCounts.rds
2.8 MB
filtering_info_featureCounts.txt
293 Bytes
histogram_plot_25_Feb_2021_featureCounts.pdf
5.5 kB
list_norm_dgls_featureCounts.rds
40.4 MB
norm_cpm_RLE_featureCounts.txt
3.0 MB
norm_cpm_TMM_featureCounts.txt
3.0 MB
norm_cpm_TMMwsp_featureCounts.txt
3.0 MB
raw_reads_fc.txt
2.9 MB
stats_fc.txt
1.2 kB
voom_plots_featureCounts.pdf
2.7 MB
voom_quality_weights_plots_featureCounts.pdf
2.5 MB
length_histogram.pdf
83.0 kB
piRNA_logos_FC_salmon.pdf
342.2 kB
piRNAs_bxplot_Testis_COLO205_treat_FC_salmon.pdf
565.4 kB
salmon
NOISeq_biodetection_25_Feb_2021_salmon.pdf
47.6 kB
NOISeq_countsbio_25_Feb_2021_salmon.pdf
404.2 kB
RLE_plots_salmon.pdf
24.6 kB
dgl_Prop_filt_salmon.rds
3.5 kB
dgl_cpm_filt_salmon.rds
3.5 kB
dgl_edgeR_salmon.rds
11.6 MB
dgl_edger_filt_batch_salmon.rds
3.0 MB
dgl_edger_filt_nobatch_salmon.rds
3.0 MB
filtering_info_salmon.txt
287 Bytes
histogram_plot_25_Feb_2021_salmon.pdf
5.6 kB
list_norm_dgls_salmon.rds
27.7 MB
norm_cpm_RLE_salmon.txt
1.5 MB
norm_cpm_TMM_salmon.txt
1.5 MB
norm_cpm_TMMwsp_salmon.txt
1.5 MB
voom_plots_salmon.pdf
1.5 MB
voom_quality_weights_plots_salmon.pdf
1.4 MB
salmon_FC_cpm_union_grouped.txt
5.8 MB
salmon_FC_cpm_union_top100.txt
47.9 kB
spike_ins_treat_FC_salmon.pdf
17.0 kB
stats_gene_types_ids.txt
384 Bytes
GRCh38_STEP_2_prep_and_quantification_COLO205_Testis_.Rmd
11.5 kB
GRCh38_STEP_3_Exploratory_Data_Analysis_Testis.Rmd
34.8 kB
GRCh38_STEP_3_Exploratory_Data_Analysis_Testis_v2.Rmd
29.6 kB
mouse_CM
EDA_mouse_cardiomyocytes_GRCm38_11_Mar_2021
featureCounts
NOISeq_biodetection_11_Mar_2021_featureCounts.pdf
10.1 kB
NOISeq_countsbio_11_Mar_2021_featureCounts.pdf
104.0 kB
annotation_fc.txt
32.6 MB
raw_reads_fc.txt
4.0 MB
stats_fc.txt
414 Bytes
length_histogram.pdf
28.2 kB
piRNA_logos_FC_salmon.pdf
100.8 kB
salmon
NOISeq_biodetection_11_Mar_2021_salmon.pdf
9.8 kB
NOISeq_countsbio_11_Mar_2021_salmon.pdf
38.5 kB
dgl_edgeR_salmon.rds
11.5 MB
salmon_FC_cpm_union_grouped.txt
219.2 kB
salmon_FC_cpm_union_top100.txt
11.7 kB
GRCm38_STEP_2_prep_and_quantification_mouse_aCM.Rmd
10.8 kB
GRCm38_STEP_3_Exploratory_Data_Analysis_mouse_aCM.Rmd
22.6 kB
Figure_workflow.jpg
1.4 MB
GRCh38_STEP1_optional.Rmd
16.1 kB
GRCh38_STEP_1_annotation_forging.Rmd
30.6 kB
GRCm38_STEP_1_annotation_forging.Rmd
31.2 kB
LICENSE
1.1 kB
README.md
1.2 kB
SraRunTable.txt
6.9 kB
WIND_LOGO.png
44.9 kB
human_data
additional_info_piRNAs_GRs
GRs_per_piRNA.txt
912.9 kB
Gene_Regions_piRNAbank_RNACentral.txt
55.9 MB
TEs_piRNAbank_rCentral_piCdb.gtf
17.4 MB
piRNA_GR_overlapping_sncRNAs_gene_types.txt
196 Bytes
sncRNA_piRNBnk_RNACent_piCdb_GRCh38_v34.gtf
43.0 MB
excluded_sncRNA_piRNBnk_RNACent_GRCh38_v34.txt
634.3 kB
piRNABank
human_pir.txt
65.2 MB
sncRNA_piRNBnk_RNACent_GRCh38_v34.fa.gz
837.9 kB
sncRNA_piRNBnk_RNACent_GRCh38_v34.gtf.gz
5.2 MB
sncRNA_spike_ins_piRNBnk_RNACent_GRCh38_v34.gtf.gz
5.1 MB
spike_ins.fasta
1.8 kB
mouse_data
piRNABank
mouse_pir.txt.gz
13.6 MB
sncRNA_piRNBnk_RNACent_GRCm38_v34.fa.gz
1.8 MB
sncRNA_piRNBnk_RNACent_GRCm38_v34.gtf.gz
31.9 MB
ping_pong.Rmd
3.2 kB