diff --git a/DESCRIPTION b/DESCRIPTION index 2590270..e589783 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Isosceles Title: Isoform Single-Cell and Long-read Expression Suite -Version: 0.1.0 +Version: 0.2.0 Authors@R: c( person("Michal", "Kabza", email = "michal.kabza@contractors.roche.com", role = c("aut", "cre")), person("Tim", "Sterne-Weiler", email = "sternewt@gene.com", role = c("aut"))) diff --git a/docs/Isosceles.html b/docs/Isosceles.html index 9f7e9a4..d9c560d 100644 --- a/docs/Isosceles.html +++ b/docs/Isosceles.html @@ -1837,7 +1837,7 @@

Introduction to the Isosceles package

*michal.kabza@contractors.roche.com
**sternewt@gene.com

8 April 2024

Package

-

Isosceles 0.1.0

+

Isosceles 0.2.0

@@ -2324,7 +2324,7 @@

11.2 Basic scRNA-Seq analysis

-

+

11.3 Identifying marker transcripts

@@ -2378,7 +2378,7 @@

11.3 Identifying marker transcrip

Top marker transcript heatmap:

dittoSeq::dittoHeatmap(sce, top_markers, annot.by = "label",
                        cluster_rows = TRUE, fontsize_row = 6)
-

+

11.4 Transcript expression UMAP plots

@@ -2393,39 +2393,39 @@

11.4 Transcript expression UMAP p }

11.4.1 ISOT-9a12-71e0-57a3-e57d:s170864850:e170870500:AP:FL

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11.4.2 ISOT-0664-96b1-953c-fbcd:s40457250:e40468600:AP:FL

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11.4.3 ISOT-222e-275a-5543-ff6e:s39312850:e39319800:AP:FL

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11.4.4 ISOT-a049-9476-caf6-f7ba:s114295800:e114312600:AP:FL

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11.4.5 ISOT-1d28-0bb1-cc79-de6b:s209675400:e209676400:AP:FL

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11.4.6 ISOT-188a-636e-edb1-889b:s29679000:e29698700:AP:FL

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11.4.7 ISOT-3d99-b5d4-4c81-952b:s150338300:e150341700:AP:FL

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11.4.8 ISOT-e3aa-f039-f992-8f8f:s105486300:e105488800:AP:FL

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11.4.9 ISOT-6639-25b4-48c3-9465:s51166550:e51171750:AP:FL

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@@ -2494,7 +2494,7 @@

12.3 PSI region visualization

-

+

Plot the CAV1 transcript structures:

plot_psi_regions(
     se_psi = se_psi,
@@ -2502,7 +2502,7 @@ 
12.3 PSI region visualization
-

+

Plot the CAV1 transcript structures with introns shrinked to max 1000 bp:

plot_psi_regions(
     se_psi = se_psi,
@@ -2511,7 +2511,7 @@ 
12.3 PSI region visualization
-

+

12.4 PSI UMAP plots

@@ -2533,51 +2533,51 @@

12.4 PSI UMAP plots

}

12.4.1 ENSG00000105974:7:116524750:+:TSS

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12.4.2 ENSG00000105974:7:116525000:+:TSS

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12.4.3 ENSG00000105974:7:116525093-116525783:+:A5

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12.4.4 ENSG00000105974:7:116525700:+:TSS

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12.4.5 ENSG00000105974:7:116525784-116525805:+:A5

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12.4.6 ENSG00000105974:7:116526250:+:TSS

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12.4.7 ENSG00000105974:7:116526389-116526524:+:RI

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12.4.8 ENSG00000105974:7:116526525-116526557:+:A3

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12.4.9 ENSG00000105974:7:116526558-116526689:+:CE

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12.4.10 ENSG00000105974:7:116559350:+:TES

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12.4.11 ENSG00000105974:7:116559550:+:TES

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12.4.12 ENSG00000105974:7:116561200:+:TES

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@@ -2606,7 +2606,7 @@

13 Session Info

## [8] base ## ## other attached packages: -## [1] Isosceles_0.1.0 SingleCellExperiment_1.18.0 +## [1] Isosceles_0.2.0 SingleCellExperiment_1.18.0 ## [3] SummarizedExperiment_1.26.1 Biobase_2.56.0 ## [5] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 ## [7] IRanges_2.30.0 S4Vectors_0.34.0 diff --git a/docs/Isosceles.pdf b/docs/Isosceles.pdf index 3e2d402..4a3b27c 100644 Binary files a/docs/Isosceles.pdf and b/docs/Isosceles.pdf differ diff --git a/docs/Mouse_E18_brain_analysis.html b/docs/Mouse_E18_brain_analysis.html index 9262c9d..a5da87f 100644 --- a/docs/Mouse_E18_brain_analysis.html +++ b/docs/Mouse_E18_brain_analysis.html @@ -3196,7 +3196,7 @@

Mouse E18 brain data analysis

*michal.kabza@contractors.roche.com
**sternewt@gene.com

8 April 2024

Package

-

Isosceles 0.1.0

+

Isosceles 0.2.0

@@ -3311,7 +3311,7 @@

2 Data exploration

arrow = arrow(ends = "last", type = "closed", length = unit(0.1, "inches")) ) -

+

Cluster cell type identities have been established using the marker gene expression signatures from the Lebrigand et al. 2020 paper:

marker_sets <- list(
@@ -3343,7 +3343,7 @@ 
2 Data exploration

       "Rad_glia", "Cyc_rad_glia", "CR_cells"),
     slot = "logcounts", size = 1
 )
-

+

3 Isoform switching

@@ -3402,7 +3402,7 @@

3 Isoform switching

plot.title = element_text(size = 12), legend.title = element_text(size = 11)) (p1 + p2) / (p3 + p4) -

+

4 DEXSeq analysis

@@ -3539,7 +3539,7 @@

4 DEXSeq analysis

plot.title = element_text(size = 12), legend.title = element_text(size = 11)) (p1 + p2) / (p3 + p4) -

+

In order to visualize the detected PSI events as a heatmap, Isosceles can calculate the PSI count to mean permuted PSI count ratios for pseudotime windows with smaller, trajectory-dependent window and step sizes (warning: @@ -3608,7 +3608,7 @@

4 DEXSeq analysis

fontsize_row = 5, treeheight_row = 0, scale = "row" ) -

+

5 Session Info

@@ -3639,7 +3639,7 @@

5 Session Info

## [9] BiocParallel_1.30.3 scuttle_1.6.2 ## [11] ggplot2_3.3.6 tibble_3.1.7 ## [13] tidyr_1.2.0 dplyr_1.0.9 -## [15] Isosceles_0.1.0 SingleCellExperiment_1.18.0 +## [15] Isosceles_0.2.0 SingleCellExperiment_1.18.0 ## [17] SummarizedExperiment_1.26.1 Biobase_2.56.0 ## [19] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 ## [21] IRanges_2.30.0 S4Vectors_0.34.0