diff --git a/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv3/out_fractions/CIBERSORTx_refsample_inferred_phenoclasses.txt b/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv3/out_fractions/CIBERSORTx_refsample_inferred_phenoclasses.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e52e2032a16c79ccce64c632dfc133eccc9fefc3
--- /dev/null
+++ b/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv3/out_fractions/CIBERSORTx_refsample_inferred_phenoclasses.txt
@@ -0,0 +1,6 @@
+B cell	1	1	1	1	1	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2
+DC	2	2	2	2	2	1	1	1	1	1	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2
+Monocyte	2	2	2	2	2	2	2	2	2	2	1	1	1	1	1	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2
+NK cell	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	1	1	1	1	1	2	2	2	2	2	2	2	2	2	2
+Other	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	1	1	1	1	1	2	2	2	2	2
+T cell	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	2	1	1	1	1	1
diff --git a/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv3/out_fractions/CIBERSORTx_sigmatrix_Adjusted.txt b/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv3/out_fractions/CIBERSORTx_sigmatrix_Adjusted.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93f6b43a5fdf87f4d9bd7ef046c23b930a58c88a
--- /dev/null
+++ b/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv3/out_fractions/CIBERSORTx_sigmatrix_Adjusted.txt
@@ -0,0 +1,2441 @@
+GeneSymbol	B cell	DC	Monocyte	NK cell	Other	T cell
+ENSG00000000938	99.30918652363867238	401.45194859987032032	759.62034970445120052	355.75224148614535125	51.75646276962967818	72.37156206485509813
+ENSG00000001561	3.06724594017615848	7.97116811836590866	7.74659805446516359	25.69484201642727683	0.00000000000000000	0.00000000000000000
+ENSG00000002587	25.78996020008730738	11.81039099069024978	0.00000000000000000	2.33812277808364755	4.21878700094443548	0.99227691413857055
+ENSG00000002933	0.00000000000000000	9.43930496490908943	109.86355048843621773	0.74637476625168409	7.70436004683326647	0.00000000000000000
+ENSG00000003249	13.98790092109139671	0.86541841093390137	0.00000000000000000	0.00000000000000000	0.89321331918021263	0.76909829706547317
+ENSG00000003436	1.16950786831787212	40.80124297546681333	12.10126584599370148	0.00000000000000000	115.60738857452304273	3.83388215244881492
+ENSG00000004468	64.08555029205244580	0.00000000000000000	8.73182169990984924	194.03558879172527440	20.07728626463664767	2.69096746226366923
+ENSG00000004799	8.19669514482688477	4.16163438228354288	50.64900700507838138	2.40789769635077722	7.45474302421701918	0.00000000000000000
+ENSG00000004939	0.00000000000000000	102.36460702302841241	53.49403480161687696	0.00000000000000000	449.12677581094999368	4.54724929455065574
+ENSG00000005187	32.50571225870455550	14.94245120105610525	12.04530482100783750	0.00000000000000000	6.76141366468065552	5.88558755036357706
+ENSG00000005243	0.00000000000000000	0.11515724851974640	0.00000000000000000	16.50804041013150325	0.00000000000000000	0.00000000000000000
+ENSG00000005249	51.55965323199826855	296.35644285825804900	105.66256035414745895	10.15468516082257366	1425.60813922280749466	32.51832521179206026
+ENSG00000005379	0.00000000000000000	31.26311469228890516	22.53747907847789733	39.78440555783837596	2.04422575928366657	4.53649903261338761
+ENSG00000005471	18.07455896141218687	3.47247314378919381	0.00000000000000000	0.00000000000000000	0.00000000000000000	0.00000000000000000
+ENSG00000005844	75.00799127779401942	77.73851133924620171	183.73219954114409802	366.00843705838002506	0.00000000000000000	142.91697756937156782
+ENSG00000005961	9.64941473528028482	111.83354148017117780	22.73415147940057679	17.68926374349218733	717.22260097074581608	8.98201882911980576
+ENSG00000006432	43.38082042175372521	0.00000000000000000	0.00000000000000000	16.88639709256541721	8.67616960184234287	8.86044170126376152
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+ENSG00000006534	22.99636058745005585	47.68916202510643387	159.37373820550584469	16.10653350926780192	0.00000000000000000	4.77925688608260746
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+ENSG00000006704	3.54628493879466511	10.71475254927884002	15.09883351613623503	0.31765478681212389	2.87774375953398209	1.01954164725757379
+ENSG00000007129	7.23321353805804712	0.00000000000000000	3.11606679477180659	5.56824321043465087	6.63831790658612242	18.12189789570096465
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+ENSG00000007264	0.25447872639297453	0.00000000000000000	1.24902835871427453	79.15728103890978673	0.00000000000000000	14.35571950372387917
+ENSG00000007312	172.28580873676020246	11.77489169862791130	3.65592227143908088	15.35761168646586050	8.90275278057159625	9.64036598972464809
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+ENSG00000007402	0.00000000000000000	1.71893480789491426	0.00000000000000000	9.35562102130009698	0.00000000000000000	2.60389120473079272
+ENSG00000007516	5.77330705965631008	2.72220651895869503	1.05591820025160388	4.22829088885704696	2.15993642073439496	1.81880619807102839
+ENSG00000007545	0.67591463312539635	0.00000000000000000	6.69182680497513260	37.74070862149670091	10.74424585647466301	9.56575428948087492
+ENSG00000008083	272.01458032677163601	388.11853113444078645	940.02175663728621657	174.94108739831307275	74.05144905299104607	77.10375628473443044
+ENSG00000008277	0.00000000000000000	0.00000000000000000	2.77669980856122267	3.44450208975202266	0.10016297876100101	4.03667550583029744
+ENSG00000008394	8.37774945636388324	37.70158689125619844	80.59748817772593554	5.05730115560785709	13.38985764193172301	0.00000000000000000
+ENSG00000008517	145.22512408041282583	0.00000000000000000	23.93386494255167563	372.73285990824393821	179.26210106540156630	885.84845418673478434
+ENSG00000009694	0.00000000000000000	0.52925163132918307	1.32914519456037783	22.44558328510099798	2.27148498838508717	6.19839888878334921
+ENSG00000010278	14.77540123509062653	17.68030205006653333	19.67732163818953950	0.00000000000000000	285.58294166781416834	4.52846377660193600
+ENSG00000010327	2.06259521041633720	13.77534594337134166	94.21135625153202398	2.12301165142692572	1.31845547292995091	0.96763798309307925
+ENSG00000010610	14.36350211601198978	93.36429781700890373	105.68886839325152494	1.05322880639981475	6.58734436116207256	46.70514399754252821
+ENSG00000010671	69.13818964656174160	20.84105031229657712	19.34333838277554918	3.45726179438639614	65.27779263392817199	2.33363185612075874
+ENSG00000011105	9.06470756633935792	0.00000000000000000	0.00000000000000000	0.00000000000000000	76.62722049456789364	1.59713609343372953
+ENSG00000011422	72.16427562499370651	554.65501607384885574	955.17804573803766743	72.21890218817274842	31.15056408353947859	17.98315705754701099
+ENSG00000011590	9.71673699744233588	0.00000000000000000	0.00000000000000000	0.00000000000000000	1.53975457072584709	0.52248534089907928
+ENSG00000011600	310.39112832056730440	2072.40275043490828466	4259.53069620533915440	2117.03783831264308901	253.15659101144308352	110.09489543123950739
+ENSG00000012124	176.94817204960855861	1.09927809705215251	22.98326015854649640	4.19894960444040866	6.95178261999008562	0.91220047298488516
+ENSG00000012779	20.67661992273083271	11.22534571166210959	24.66050168231021544	1.27770461966941906	1.32659865751052086	0.00000000000000000
+ENSG00000013016	21.62386910971960674	16.66165650923615971	7.21080239034202908	2.82192331585442524	130.84064318080518774	4.06087250610497374
+ENSG00000013392	3.86098287962002029	2.06875506773428164	0.00000000000000000	0.00000000000000000	0.00000000000000000	3.45724801282340133
+ENSG00000013725	23.15462980440542395	0.00000000000000000	8.90840901949571951	33.48233029572671171	49.63916229366255806	164.46323317810549725
+ENSG00000014257	3.34749357937666536	25.13286887885717391	25.63516997704546441	4.29722967267287981	3.35639830347161672	0.40050650100540947
+ENSG00000014914	8.16143610548389553	27.02199054879387319	30.41237509153289409	6.89237602202159039	0.00000000000000000	1.01995149095931525
+ENSG00000017427	6.08341887210919552	0.00000000000000000	0.00000000000000000	0.00000000000000000	0.11567344444506103	0.00000000000000000
+ENSG00000018280	137.70391337545470378	70.04870959958370236	1244.66651894930873823	103.30105163605567498	0.00000000000000000	12.11394548240410529
+ENSG00000019102	0.00000000000000000	0.91512308638093431	2.16376252601538344	0.36852111898095108	5.26989349065291357	0.00000000000000000
+ENSG00000019169	1.80219901029304763	15.58652423102144979	47.64795486801078539	5.34592954518042873	1.40467504167949264	0.36110120411718760
+ENSG00000019582	9643.89905751490186958	10512.19168876971525606	3001.62232656290098021	1401.52075692331027312	788.40175103648198274	593.32274359032385291
+ENSG00000020577	6.22131940557627150	4.54333751006378250	20.97057519429769457	0.00000000000000000	6.26205391202510508	0.49373871044391487
+ENSG00000020633	73.79561391748694632	11.13700554863602932	58.80377573324332019	691.01965342194546338	73.34043104194988416	231.61717554911774641
+ENSG00000021300	3.11524560287750374	0.00000000000000000	0.00000000000000000	0.00000000000000000	6.81455312546239167	20.50449930255454944
+ENSG00000021762	0.38610306483908269	0.00000000000000000	17.79052694988114425	103.82777764836035317	6.39658425764076100	17.75350975283268440
+ENSG00000022267	4.34758788685024111	14.92338391327672475	10.69622410692695347	1.57514727652886810	143.33850739663279228	6.48347189685368885
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+ENSG00000023445	208.43839607850676998	24.55698083182337754	23.44817486321507616	22.00757521233070335	47.27797205777880407	107.54778603701734596
+ENSG00000025708	140.58733885757132498	726.53249843513560791	1429.01897762002386116	148.23877985740600138	164.69428920443039033	67.03309565549180604
+ENSG00000026559	35.30881113513621727	0.00000000000000000	3.95926737762328873	5.89054903404512853	0.00000000000000000	2.72459016961306455
+ENSG00000026751	38.15630104875241102	62.51273038411916616	8.09088362671629113	122.18929072900709798	6.06581852299421165	23.42654044218707909
+ENSG00000027075	32.45552417806342049	0.00000000000000000	31.57316550525404608	316.63645451639445128	40.18555717918112435	160.66222454006023668
+ENSG00000027869	17.88101942519460152	5.32457278225327890	13.11476243245953377	164.12903280048359989	0.00000000000000000	58.52878558611806170
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+ENSG00000030419	10.53272488455834655	12.62249312694469161	6.60939659200494933	40.87221168113575942	7.22333808098644425	26.02128557291239375
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+ENSG00000035862	64.92076864225592203	268.42463628673266385	495.11086029156655286	17.23293801599944075	49.77257877164560540	35.17207640505625221
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+ENSG00000038945	0.00000000000000000	3.55401147767437164	27.57245726455328594	0.00000000000000000	3.44952220585808833	0.00000000000000000
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+ENSG00000042980	108.47319501088362870	28.05929462721753964	16.66797703498642491	10.87819855175325934	0.00000000000000000	0.00000000000000000
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+ENSG00000285043	0.00000000000000000	0.00000000000000000	0.00000000000000000	0.25897740086038740	10.06422955961437005	0.00000000000000000
diff --git a/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv4/out_fractions/CIBERSORTx_Adjusted.txt b/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv4/out_fractions/CIBERSORTx_Adjusted.txt
new file mode 100644
index 0000000000000000000000000000000000000000..256cf8f3b21c5fbebe4ed1d4ccb843200778ea2f
--- /dev/null
+++ b/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv4/out_fractions/CIBERSORTx_Adjusted.txt
@@ -0,0 +1,7 @@
+Mixture	B cell	DC	Monocyte	NK cell	Other	T cell	P-value	Correlation	RMSE
+N138_TOL	0.00000000000000000	0.04114279358384821	0.11936285456123433	0.05761437009962719	0.73979836846796687	0.04208161328732340	9999.00000000000000000	0.60134549917378488	1.34435362932035662
+N138_FU1	0.00000000000000000	0.09490818540378067	0.14124595029847198	0.06717062499916213	0.66388583376339017	0.03278940553519501	9999.00000000000000000	0.72834333389072448	1.04233221834684686
+N129_BC	0.00000000000000000	0.13028223908447134	0.15812651463277935	0.07408672146937831	0.34267290155896563	0.29483162325440548	9999.00000000000000000	0.70289787340644128	0.71792928529770372
+N129_AC	0.00000000000000000	0.12593171903949169	0.11216195654320209	0.09680478784163916	0.38616493430000726	0.27893660227565975	9999.00000000000000000	0.63055318544081407	0.81860723407801383
+N147_TOL	0.00000000000000000	0.05229539613055165	0.22249588472983833	0.05370046601599323	0.49030845119542116	0.18119980192819565	9999.00000000000000000	0.87844142207026976	0.54240721154140814
+N159_BC	0.00000000000000000	0.03659375882086248	0.07371234637525637	0.00000000000000000	0.41001165596676226	0.47968223883711886	9999.00000000000000000	0.95093966631821525	0.30948271100128805
diff --git a/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv4/out_fractions/CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt b/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv4/out_fractions/CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad2b0467afd02aaca08a7519982e5797f6b5885f
--- /dev/null
+++ b/paper-releases/pbisc-diffusion/updates/20261008T022410Z-deconv-scsemi-deck/diffusion/dataset/server_1/model8/plans/bayesprism_paired_20261006/cibersortx/ji2025_chili/cv4/out_fractions/CIBERSORTx_refsample_inferred_phenoclasses.CIBERSORTx_refsample_inferred_refsample.bm.K999.txt
@@ -0,0 +1,2407 @@
+NAME	B cell	DC	Monocyte	NK cell	Other	T cell
+ENSG00000002587	10.80138812727191500	14.20444938703008830	1.00000000000000000	1.00000000000000000	3.38663484486873578	1.00000000000000000
+ENSG00000002745	5.64948513125917984	1.00000000000000000	1.00000000000000000	1.00000000000000000	1.00000000000000000	1.00000000000000000
+ENSG00000002933	1.00000000000000000	5.03719190090550573	74.44622148755146895	1.00000000000000000	1.76266015863331793	1.00000000000000000
+ENSG00000003249	13.48196430553552538	1.00000000000000000	1.00000000000000000	1.00000000000000000	1.00000000000000000	5.80568647496697654
+ENSG00000003436	1.00000000000000000	2.73768289335044868	2.55617802676626660	1.00000000000000000	57.73898307167914368	1.00000000000000000
+ENSG00000004139	8.70733325114040113	3.45821042281219437	3.58341406091320858	29.85804410967923417	10.32124383092752851	9.46770238837969025
+ENSG00000004468	122.98039415868075253	35.95333056985271014	12.25219524118546133	178.68081319780657168	36.76543440080215674	24.54978236072859943
+ENSG00000004799	2.22219506233195219	7.03806589949531869	25.23779697593914406	1.00000000000000000	4.24806214426941775	1.00000000000000000
+ENSG00000004838	1.00000000000000000	1.00000000000000000	1.00000000000000000	8.01288390703408204	1.49627791563275458	1.00000000000000000
+ENSG00000004939	1.00000000000000000	1.00000000000000000	1.00000000000000000	1.00000000000000000	30.38290026255519294	1.00000000000000000
+ENSG00000005187	46.40433604819055091	7.40281969382393168	1.00000000000000000	4.65975646174117308	19.84238003357847546	6.24642953658974154
+ENSG00000005243	1.00000000000000000	1.51177072671443247	5.54675943997306931	32.75219652073451471	2.07020547945204925	8.00869946772991881
+ENSG00000005249	22.12165195676891827	61.20250403799573036	60.99841078605276579	5.53059244318094567	2714.00593186798505485	5.17727055861310514
+ENSG00000005381	1.00000000000000000	1.00000000000000000	5.62389904926014417	1.00000000000000000	1.00000000000000000	1.00000000000000000
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