From 2422cffe29a44eea95e9401689c760d251a67dac Mon Sep 17 00:00:00 2001 From: Michal Kabza Date: Fri, 28 Jul 2023 14:14:43 -0700 Subject: [PATCH] Bumped the version to 0.0.2 --- DESCRIPTION | 2 +- docs/Isosceles.html | 60 ++++++++++++++++++++++---------------------- docs/Isosceles.pdf | Bin 96154 -> 96151 bytes 3 files changed, 31 insertions(+), 31 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f04c363..1397feb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Isosceles Title: Isoform Single-Cell and Long-read Expression Suite -Version: 0.0.1.9000 +Version: 0.0.2 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 fd843df..147a052 100644 --- a/docs/Isosceles.html +++ b/docs/Isosceles.html @@ -10,7 +10,7 @@ - + Introduction to the Isosceles package @@ -1835,9 +1835,9 @@

Introduction to the Isosceles package

Michal Kabza1* and Tim Sterne-Weiler2,3**

1Roche Informatics, F. Hoffmann-La Roche Ltd., Poznań, Poland
2Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, USA
3Department of Discovery Oncology, Genentech Inc., South San Francisco, USA

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

-

27 July 2023

+

28 July 2023

Package

-

Isosceles 0.0.1.9000

+

Isosceles 0.0.2

@@ -2218,7 +2218,7 @@

6.2 Basic scRNA-Seq analysis

size = 2, main = "", do.label = TRUE, labels.highlight = TRUE, legend.show = FALSE) -

+

6.3 Identifying marker transcripts

@@ -2272,7 +2272,7 @@

6.3 Identifying marker transcript

Top marker transcript heatmap:

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

+

6.4 Transcript expression UMAP plots

@@ -2287,39 +2287,39 @@

6.4 Transcript expression UMAP pl }

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

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+

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

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

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

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

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

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

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

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

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+

@@ -2406,7 +2406,7 @@

7.3 PSI region visualization

treeheight_row = 0, annotation_names_col = FALSE, annotation_colors = list(region = region_colors) ) -

+

Plot the CAV1 transcript structures:

# Calculate the relative expression of transcripts based on overall TPM values
 # across all cells
@@ -2467,7 +2467,7 @@ 
7.3 PSI region visualization

     heights = c(0.1, 0.8, 0.1),
     label.text.cex = 0.7
 )
-

+

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

# Prepare the shrinkage function
 region_granges_list <- GRangesList(PSI = rowRanges(se_psi))
@@ -2523,7 +2523,7 @@ 
7.3 PSI region visualization

     heights = c(0.1, 0.8, 0.1),
     label.text.cex = 0.7
 )
-

+

7.4 PSI UMAP plots

@@ -2545,51 +2545,51 @@

7.4 PSI UMAP plots

}

7.4.1 ENSG00000105974:7:116524750:+:TSS

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7.4.2 ENSG00000105974:7:116525000:+:TSS

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

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7.4.4 ENSG00000105974:7:116525700:+:TSS

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

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7.4.6 ENSG00000105974:7:116526250:+:TSS

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

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

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

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7.4.10 ENSG00000105974:7:116559350:+:TES

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7.4.11 ENSG00000105974:7:116559550:+:TES

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7.4.12 ENSG00000105974:7:116561200:+:TES

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@@ -2618,7 +2618,7 @@

8 Session Info

## [8] base ## ## other attached packages: -## [1] Isosceles_0.0.1.9000 SingleCellExperiment_1.18.0 +## [1] Isosceles_0.0.2 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 fb009e1b5b0fa967955914e7439eb0aab85ff285..f7ee4f28d05aa74f0878e38571cd89df50134a8c 100644 GIT binary patch delta 1459 zcmV;k1x)&y?**6d1&|~HH8qnEE-8PNmPwD(Fc^mK^DA;Am8Ql^)&ockv#29LsI9m# zNVticS~v@~BTf1BICZ8_#&L&J-6YTVzTXl%FsK3;++Dzl->db->syQi3_+6MI9P83 zj4{A*8pLS^k}O!4!PoHf48f2VKWN2fa~#9)`$Dy@AD4%W(lQ8R(;%gOwcQ2~LJ6bCePg<;W~D012^y)-#laTnqLu zO8!D|1X7%uI|sy=-L|r}sw>`9g3aGEA?yX(ly>o;$q1<0g2I)(rO?A02dw^|muW~z|9(`S_82w;*tDXnKD z4kc|YYBMdFW`#Z`ek{<>o;I34K!^+a=k`{%V`+scpj{1BRKT0SXyc?<*Q{erseJAu zGg>C$(f!iOJ-`^gePh=qEP&<$x*WnB;wNxu%3(Y$W@lg+0n=nAdCh+s{X7x^!`uy_ z&UHP9=}9LRb=OMm&4c6s=j17mUUQ*dkV^zemYn8NGreoe^DrE-#9~TQ{c>p3l7c>U z__RK%Mkb0=~xT((Hc#%<0y&=!_^Yrf4%D znTK8~TI;qIPF;l0>%J4bYKC22O=LVhol;Blx<5B93B zYbyCKR{GB=>@&eDNxPjhZ_lo+ie77RcC$GiZvisji%}XKzWOj65A@TM^JabV8#@Vz ziV9_JWOHMKLrsH$*cqFgQ3dML0q}AUr`aLqjk|Fg8LqLNhc*Ml&`=F*G(e zL^CijI5;syI6^*M3NK7$ZfA68AT={LlMpT`e;t##QdChCMbEiy3nJPIA}WZjAfPQG zj(~vk01hC|iX(|BrMZDs2D{4AP^-Rng}{3{V9 zGJ3xT)kF(=K$W0?Q>@*ms(=mP9BcQes$e6y!rEP`HqZ{1SX-vr1UdlYb%$y*=malW ze`9mm0=Clfa4pi-z&2XrHtlxMMY{*wqU{DdXpe)Nv^`)a=mmWlQS(uEf!)9ZE`iJ7 zI%|8u0N4lWU_Uqj2Eht^sbmaMW@FoCK%Ae;F_drr76G&VYGvHlyQ#A$SBHgD2n_ldaTBM%QnTdI4U6 z*I<<`{GdwaYTXsW34K(}7+Cij)(Pu`Yr-{gUZIchN_L|&WALN@fkU!Gm?JC^197V- zm)mv$Ab$Z6L_{m16&}celA!7tV}JZyLJ@(AWaMvi9PmdF43uPU5xvHDwn}6n?i5(b}0SxXg;Kc9M=Hm4&#sP*PNpKu& zb^*p1;5ZH9bODk@uqlGC;pZ8GAd7Uy>*^K@QHJoC+x~A&AE}o7(M3gb zG-=-zZ*p_Y#37Yb2qs)S@%6h8@QLwqzip&)HZSscx{l07jZkPB@5GI=5AVhASZ#KZ z+zCh64=ZC?T`Jd%Cz0m`zFL>8ZYuXU_!7Pwuw}h#uD4FBv1fmnmMgOZFlV-=MQ22L zK1G`WS$OD`qLpqM;nYR=yzV=}%evp?)kMY9(Ms-lwrVuk;l!oDPUDQUZR*6rD~Ro-bW&Tclx<1IkuqcKXO;nNSp@jyR4Id3)> zzX84JiGK=ZZe)W*1Ghv20Z(rSH!(LeH8eMunsNag2RAV{Gc`0fx4m)!Ap%iCH#j&# zIX6T#I7K)?G(|BvLODZ1IYlx-Gc+?dLPjt?AUr}hI5|gkhS~;zre)U%*6R2CKl(qC)e8hInUYe`#kscMnwE85hXHu zJ_psY7W9BBK>?>&TcoOhb>KW}_o=F2J-E!;J*qaa0o-M6fodaY2aMM|)h5sZp0UQ} zf3g{Dq2=MaLt6u#w8m}Pt)Po`7q~^c4Q!`94sOzRgB_p;^kqcNN9_eWfd|ZjOW+!7 zyTJh10|vofFa(CdJ}?6Ig9G3&I0X7LDocLQC_`t!721Pf95jGm{0YDM(7dEbp^Ske zU=q|b+8UmBlr2{QH(oeuIRQ?B)8Gs^e+wqq=TlCB>)>2Q`zMc@1{c6Zz)Kb`qHqz# zugil9S0Wp61NdT>!CXe|rAIjwr{!p!xn-~=)@KPk1dqUDu*zgBwUW{G+oPU>=imic zV+%j1lDRhG3gLu4s%8xQ@EX<$>x65?50Xvu2 zb^#!N4iH2{E20%1$bpie1~bO~__>540u{-~-yqS7XhpP|$Qb|Y&662#f4OQ!`=Qs> zRL1u&t{R!uudb#u>mObD`<(*>Dv}Y&h-5@EB44clXJkc5M*dcbN5muIX-4MjMJ6|~ tq{*k-Y^C+;TkD56@8Uo8qI2^KWo~41baG{vcXt672{tqeB_%~qMhdXWn~MMd