From b351c24c2b5a49e429ec9afeb50ec541e053b5b3 Mon Sep 17 00:00:00 2001
From: RubD <rubendries@gmail.com>
Date: Thu, 20 Apr 2023 11:40:21 -0400
Subject: [PATCH] remove unnecessary files and folders

---
 inst/extdata/datasets.txt               |   15 -
 inst/extdata/mouse_ligand_receptors.txt | 1068 -----------------------
 inst/extdata/sig_matrix.txt             |  875 -------------------
 vignettes/.gitignore                    |    2 -
 4 files changed, 1960 deletions(-)
 delete mode 100644 inst/extdata/datasets.txt
 delete mode 100644 inst/extdata/mouse_ligand_receptors.txt
 delete mode 100644 inst/extdata/sig_matrix.txt
 delete mode 100644 vignettes/.gitignore

diff --git a/inst/extdata/datasets.txt b/inst/extdata/datasets.txt
deleted file mode 100644
index 94a0856b8..000000000
--- a/inst/extdata/datasets.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-dataset	spatial_locs	expr_matrix	metadata
-ST_OB1	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2016_ST_olfactory_bulb/cell_locations/Rep11_MOB_0_location.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2016_ST_olfactory_bulb/count_matrix/Rep11_MOB_0_expr.txt
-ST_OB2	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2016_ST_olfactory_bulb/cell_locations/Rep12_MOB_0_location.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2016_ST_olfactory_bulb/count_matrix/Rep12_MOB_0_expr.txt
-codex_spleen	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_codex_spleen/cell_locations/codex_BALBc_3_coord.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_codex_spleen/count_matrix/codex_BALBc_3_expression.txt.gz	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_codex_spleen/cell_locations/codex_BALBc_3_annotation.txt|https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_codex_spleen/cell_locations/cell_type_annotation.csv
-cycif_PDAC	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_CyCIF_PDAC/cell_locations/cyCIF_PDAC_coord.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_CyCIF_PDAC/count_matrix/cyCIF_PDAC_expression.txt.gz	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_CyCIF_PDAC/cell_locations/cyCIF_PDAC_annot.txt|https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_CyCIF_PDAC/raw_data/canvas.png
-starmap_3D_cortex	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_starmap_3D_cortex/cell_locations/STARmap_3D_data_cell_locations.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_starmap_3D_cortex/count_matrix/STARmap_3D_data_expression.txt
-osmfish_SS_cortex	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_osmFISH_SScortex/cell_locations/osmFISH_prep_cell_coordinates.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_osmFISH_SScortex/count_matrix/osmFISH_prep_expression.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_osmFISH_SScortex/raw_data/osmFISH_prep_cell_metadata.txt
-merfish_preoptic	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_merFISH_science_hypo_preoptic/cell_locations/merFISH_3D_data_cell_locations.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_merFISH_science_hypo_preoptic/count_matrix/merFISH_3D_data_expression.txt.gz	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2018_merFISH_science_hypo_preoptic/cell_locations/merFISH_3D_metadata.txt
-seqfish_SS_cortex	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2019_seqfish_plus_SScortex/cell_locations/cortex_svz_centroids_coord.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2019_seqfish_plus_SScortex/count_matrix/cortex_svz_expression.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2019_seqfish_plus_SScortex/cell_locations/cortex_svz_centroids_annot.txt
-seqfish_OB	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2019_seqfish_plus_olfactory_bulb/cell_locations/OB_centroids_coord.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2019_seqfish_plus_olfactory_bulb/count_matrix/OB_expression.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2019_seqfish_plus_olfactory_bulb/cell_locations/OB_centroids_annot.txt
-slideseq_cerebellum	https://zenodo.org/record/4034228/files/BeadLocationsForR.csv	https://zenodo.org/record/4034228/files/MappedDGEForR.csv	https://zenodo.org/record/4034228/files/l1.cerebellum.cellID.txt|https://zenodo.org/record/4034228/files/l1.cerebellum.cells.nonblood.txt|https://zenodo.org/record/4034228/files/l1.cerebellum.cells.txt|https://zenodo.org/record/4034228/files/l1.cerebellum.class.txt|https://zenodo.org/record/4034228/files/l1.cerebellum.genes.txt|https://zenodo.org/record/4034228/files/l1.cerebellum.txt
-ST_SCC	https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_1_spatial_locs.csv|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_2_spatial_locs.csv|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/cell_locations/P2_3_spatial_locs.csv	https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_1_expression.csv|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_2_expression.csv|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/count_matrix/P2_3_expression.csv	https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/p2_metadata.rds|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/scrna_expr.rds|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/normalized_sc_matrix.RDS|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/cell_type_vector.RDS|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/scRNAseq/sign_list.RDS|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/lowres_images/P2_1_0.0625.jpg|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/lowres_images/P2_2_0.0625.jpg|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/lowres_images/P2_3_0.0625.jpg|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/imgReg.zip|https://github.com/drieslab/spatial-datasets/raw/master/data/2020_ST_SCC/PairsLigRec.txt
-Human_PCa_scRNAseq		https://github.com/drieslab/spatial-datasets/raw/master/data/2022_scRNAseq_human_prostate/count_matrix/prostate_sc_expression_matrix.csv.gz	https://github.com/drieslab/spatial-datasets/raw/master/data/2022_scRNAseq_human_prostate/cell_metadata/prostate_sc_metadata.csv
-Mouse_brain_scRNAseq		https://github.com/drieslab/spatial-datasets/raw/master/data/2022_scRNAseq_mouse_brain/count_matrix/brain_sc_expression_matrix.txt.gz	https://github.com/drieslab/spatial-datasets/raw/master/data/2022_scRNAseq_mouse_brain/cell_metadata/brain_sc_metadata.csv
-mini_seqFISH	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2022_miniseqFISH/seqfish_field_locs.txt	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2022_miniseqFISH/seqfish_field_expr.txt.gz	https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2022_miniseqFISH/mouse_ligand_receptors.txt
diff --git a/inst/extdata/mouse_ligand_receptors.txt b/inst/extdata/mouse_ligand_receptors.txt
deleted file mode 100644
index cf82b41b8..000000000
--- a/inst/extdata/mouse_ligand_receptors.txt
+++ /dev/null
@@ -1,1068 +0,0 @@
-mouseLigand	mouseReceptor
-A2m	Lrp1
-Aanat	Mtnr1a
-Aanat	Mtnr1b
-Adam12	Itga9
-Adam12	Itgb1
-Adam12	Sdc4
-Adam15	Itga5
-Adam15	Itga9
-Adam15	Itgb1
-Adam15	Itgb3
-Adam17	Itga5
-Adam17	Itgb1
-Adam23	Itga5
-Adam23	Itgb3
-Adam2	Itga6
-Adam2	Itgb1
-Adam9	Itga6
-Adam9	Itgav
-Adam9	Itgb1
-Adam9	Itgb5
-Adcyap1	Adcyap1r1
-Adcyap1	Vipr1
-Adcyap1	Vipr2
-Adipoq	Adipor1
-Adipoq	Adipor2
-Adm2	Calcr
-Adm2	Calcrl
-Adm2	Ramp1
-Adm	Calcr
-Adm	Calcrl
-Adm	Gpr182
-Adm	Mrgprx2
-Adm	Ramp2
-Agrn	Musk
-Agrp	Mc3r
-Agrp	Mc4r
-Agrp	Mc5r
-Agt	Agtr1
-Agt	Agtr2
-Agt	Lrp2
-Agt	Mas1
-Amh	Amhr2
-Angpt1	Tek
-Angpt1	Tie1
-Angpt2	Tek
-Angpt4	Tek
-Angptl1	Tek
-Anxa1	Fpr1
-Anxa1	Fpr2
-Anxa1	Fpr3
-Apln	Aplnr
-Apob	Ldlr
-Apoe	Ldlr
-Apoe	Lrp5
-Apoe	Lrp8
-Apoe	Sorl1
-Apoe	Vldlr
-App	Fpr2
-Aregb	Egfr
-Areg	Egfr
-Arf1	Pld2
-Artn	Gfra3
-Artn	Ret
-Asip	Atrn
-Asip	Mc1r
-Avp	Avpr1a
-Avp	Avpr1b
-Avp	Avpr2
-Avp	Oxtr
-Bdnf	Ngfr
-Bdnf	Ngfrap1
-Bdnf	Ntrk2
-Bmp10	Acvr2a
-Bmp10	Acvrl1
-Bmp10	Bmpr1a
-Bmp10	Bmpr1b
-Bmp10	Bmpr2
-Bmp15	Acvr2a
-Bmp15	Bmpr1a
-Bmp15	Bmpr1b
-Bmp15	Bmpr2
-Bmp2	Acvr1
-Bmp2	Acvr2a
-Bmp2	Acvr2b
-Bmp2	Bmpr1a
-Bmp2	Bmpr1b
-Bmp2	Bmpr2
-Bmp3	Acvr2b
-Bmp4	Bmpr1a
-Bmp4	Bmpr1b
-Bmp4	Bmpr2
-Bmp5	Bmpr1a
-Bmp6	Acvr1
-Bmp6	Acvr2a
-Bmp6	Bmpr1a
-Bmp6	Bmpr1b
-Bmp6	Bmpr2
-Bmp7	Acvr1
-Bmp7	Acvr2a
-Bmp7	Acvr2b
-Bmp7	Bmpr1a
-Bmp7	Bmpr1b
-Bmp7	Bmpr2
-Btc	Egfr
-Btc	Erbb3
-Btc	Erbb4
-Btla	Tnfrsf14
-C3	C3ar1
-C3	Itgax
-C3	Itgb2
-C3	Lrp1
-C5	C5ar1
-C5	C5ar2
-Calca	Calcr
-Calca	Calcrl
-Calca	Ramp1
-Calcb	Calcr
-Calcb	Calcrl
-Calcb	Ramp1
-Calr	Scarf1
-Camp	Fpr2
-Cck	Cckar
-Cck	Cckbr
-Ccl11	Ackr2
-Ccl11	Ccr2
-Ccl11	Ccr3
-Ccl11	Ccr5
-Ccl11	Cxcr3
-Ccl13	Ackr2
-Ccl13	Ccr1
-Ccl13	Ccr2
-Ccl13	Ccr3
-Ccl13	Ccr5
-Ccl13	Cxcr3
-Ccl14	Ackr2
-Ccl14	Ccr1
-Ccl14	Ccr5
-Ccl15	Ccr1
-Ccl15	Ccr3
-Ccl16	Ccr1
-Ccl16	Ccr2
-Ccl16	Ccr5
-Ccl16	Hrh4
-Ccl17	Ccr4
-Ccl17	Ccr8
-Ccl19	Ackr4
-Ccl19	Ccr7
-Ccl19	Ccrl2
-Ccl19	Cxcr3
-Ccl1	Ccr8
-Ccl20	Ccr6
-Ccl20	Cxcr3
-Ccl21	Ackr4
-Ccl21	Ccr7
-Ccl21	Cxcr3
-Ccl22	Ccr4
-Ccl23	Ccr1
-Ccl24	Ccr2
-Ccl24	Ccr3
-Ccl25	Ackr4
-Ccl25	Ccr9
-Ccl26	Ccr2
-Ccl26	Ccr3
-Ccl27	Ccr10
-Ccl28	Ccr10
-Ccl28	Ccr3
-Ccl2	Ackr2
-Ccl2	Ccr1
-Ccl2	Ccr2
-Ccl2	Ccr3
-Ccl2	Ccr4
-Ccl2	Ccr5
-Ccl2	Darc
-Ccl3	Ccr1
-Ccl3	Ccr5
-Ccl4	Ackr2
-Ccl4	Ccr1
-Ccl4	Ccr5
-Ccl4	Ccr8
-Ccl5	Ackr2
-Ccl5	Ccr1
-Ccl5	Ccr3
-Ccl5	Ccr4
-Ccl5	Ccr5
-Ccl5	Cxcr3
-Ccl5	Darc
-Ccl5	Gpr75
-Ccl7	Ackr2
-Ccl7	Ccr1
-Ccl7	Ccr2
-Ccl7	Ccr3
-Ccl7	Ccr5
-Ccl7	Cxcr3
-Ccl8	Ackr2
-Ccl8	Ccr1
-Ccl8	Ccr2
-Ccl8	Ccr3
-Ccl8	Ccr5
-Cd24	Selp
-Cd34	Sell
-Cd40lg	Cd40
-Cd55	Cd97
-Cd70	Cd27
-Cdh1	Itgae
-Cdh1	Itgb7
-Cfh	Sell
-Cga	Fshr
-Cga	Lhcgr
-Cga	Tshr
-Cgb	Lhcgr
-Chad	Itga2
-Chad	Itgb1
-Clcf1	Cntfr
-Clcf1	Crlf1
-Clcf1	Il6st
-Clcf1	Lifr
-Cntf	Cntfr
-Cntf	Il6st
-Cntf	Lifr
-Col18a1	Gpc1
-Col18a1	Itga5
-Col18a1	Itgb1
-Col1a1	Ddr1
-Col1a1	Ddr2
-Col1a1	Itga11
-Col1a1	Itga2
-Col1a1	Itgb1
-Col2a1	Itga10
-Col2a1	Itga2
-Col2a1	Itgb1
-Col4a1	Itga1
-Col4a1	Itgb1
-Col4a1	Itgb8
-Col5a3	Sdc3
-Cort	Ghsr
-Cort	Mrgprx2
-Cort	Sstr1
-Cort	Sstr2
-Cort	Sstr3
-Cort	Sstr4
-Cort	Sstr5
-Crh	Crhr1
-Crh	Crhr2
-Crh	Mc2r
-Csf1	Csf1r
-Csf2	Csf1r
-Csf2	Csf2ra
-Csf2	Csf2rb
-Csf2	Csf3r
-Csf3	Csf1r
-Csf3	Csf3r
-Csh1	Prlr
-Csh2	Prlr
-Cshl1	Prlr
-Ctf1	Il6st
-Ctf1	Lifr
-Ctgf	Itgam
-Ctgf	Itgb2
-Ctgf	Lrp6
-Cx3cl1	Cx3cr1
-Cxcl10	Ccr3
-Cxcl10	Cxcr3
-Cxcl11	Ackr3
-Cxcl11	Ccr3
-Cxcl11	Cxcr3
-Cxcl12	Ackr3
-Cxcl12	Cxcr3
-Cxcl12	Cxcr4
-Cxcl13	Cxcr5
-Cxcl16	Cxcr6
-Cxcl1	Cxcr1
-Cxcl1	Cxcr2
-Cxcl1	Darc
-Cxcl2	Cxcr1
-Cxcl2	Cxcr2
-Cxcl2	Xcr1
-Cxcl3	Cxcr1
-Cxcl3	Cxcr2
-Cxcl5	Cxcr1
-Cxcl5	Cxcr2
-Cxcl6	Cxcr1
-Cxcl6	Cxcr2
-Cxcl9	Ccr3
-Cxcl9	Cxcr3
-Cyr61	Itga5
-Cyr61	Itgam
-Cyr61	Itgb2
-Cyr61	Itgb3
-Defb4a	Ccr6
-Defb4b	Ccr6
-Dhh	Hhip
-Dhh	Ptch2
-Dkk1	Kremen1
-Dkk1	Kremen2
-Dkk1	Lrp6
-Dkk2	Lrp6
-Dlk1	Notch1
-Dll1	Notch1
-Dll1	Notch2
-Dll1	Notch3
-Dll4	Notch1
-Dll4	Notch2
-Dll4	Notch3
-Dll4	Notch4
-Eda	Eda2r
-Eda	Edar
-Edn1	Ednra
-Edn2	Ednra
-Edn3	Ednrb
-Efna1	Epha1
-Efna1	Epha2
-Efna1	Epha3
-Efna1	Epha4
-Efna1	Epha5
-Efna1	Epha6
-Efna1	Epha7
-Efna1	Epha8
-Efna2	Epha2
-Efna2	Epha3
-Efna2	Epha4
-Efna2	Epha5
-Efna2	Epha6
-Efna2	Epha7
-Efna2	Epha8
-Efna3	Epha1
-Efna3	Epha2
-Efna3	Epha3
-Efna3	Epha4
-Efna3	Epha5
-Efna3	Epha6
-Efna3	Epha7
-Efna3	Epha8
-Efna3	Ephb1
-Efna4	Epha2
-Efna4	Epha3
-Efna4	Epha4
-Efna4	Epha5
-Efna4	Epha6
-Efna4	Epha7
-Efna4	Epha8
-Efna5	Epha2
-Efna5	Epha3
-Efna5	Epha4
-Efna5	Epha5
-Efna5	Epha6
-Efna5	Epha7
-Efna5	Epha8
-Efna5	Ephb2
-Efnb1	Ephb1
-Efnb1	Ephb2
-Efnb1	Ephb3
-Efnb1	Ephb4
-Efnb1	Ephb6
-Efnb2	Epha4
-Efnb2	Ephb1
-Efnb2	Ephb2
-Efnb2	Ephb3
-Efnb2	Ephb4
-Efnb2	Ephb6
-Efnb3	Epha4
-Efnb3	Ephb2
-Efnb3	Ephb3
-Efnb3	Ephb4
-Egf	Egfr
-Epgn	Egfr
-Epo	Epor
-Ereg	Egfr
-Ereg	Erbb4
-F2	F2r
-F2	F2rl1
-F2	F2rl2
-F2	F2rl3
-F7	F3
-F8	Lrp1
-F9	Lrp1
-Faslg	Fas
-Faslg	Tnfrsf6b
-Fga	Itgax
-Fga	Itgb2
-Fgf10	Fgfr2
-Fgf16	Fgfr2
-Fgf16	Fgfr3
-Fgf16	Fgfr4
-Fgf17	Fgfr1
-Fgf17	Fgfr2
-Fgf17	Fgfr3
-Fgf17	Fgfr4
-Fgf18	Fgfr1
-Fgf18	Fgfr2
-Fgf18	Fgfr3
-Fgf18	Fgfr4
-Fgf19	Fgfr1
-Fgf19	Fgfr2
-Fgf19	Fgfr3
-Fgf19	Fgfr4
-Fgf1	Fgfr1
-Fgf1	Fgfr2
-Fgf1	Fgfr3
-Fgf1	Fgfr4
-Fgf22	Fgfr2
-Fgf23	Fgfr1
-Fgf23	Fgfr2
-Fgf23	Fgfr4
-Fgf2	Fgfr1
-Fgf2	Fgfr2
-Fgf2	Fgfr3
-Fgf2	Fgfr4
-Fgf2	Sdc2
-Fgf2	Sdc4
-Fgf3	Fgfr1
-Fgf3	Fgfr2
-Fgf4	Fgfr1
-Fgf4	Fgfr2
-Fgf4	Fgfr3
-Fgf4	Fgfr4
-Fgf5	Fgfr1
-Fgf5	Fgfr2
-Fgf5	Fgfr3
-Fgf5	Fgfr4
-Fgf6	Fgfr1
-Fgf6	Fgfr2
-Fgf6	Fgfr4
-Fgf7	Fgfr2
-Fgf8	Fgfr1
-Fgf8	Fgfr2
-Fgf8	Fgfr3
-Fgf8	Fgfr4
-Fgf9	Fgfr1
-Fgf9	Fgfr2
-Fgf9	Fgfr3
-Fgf9	Fgfr4
-Figf	Flt4
-Figf	Kdr
-Figf	Nrp2
-Flt3lg	Flt3
-Fn1	Itga2
-Fn1	Itga2b
-Fn1	Itga4
-Fn1	Itga5
-Fn1	Itga8
-Fn1	Itgb1
-Fn1	Itgb3
-Fn1	Itgb6
-Fn1	Itgb8
-Fn1	Sdc2
-Fshb	Fshr
-Galp	Galr1
-Galp	Galr2
-Galp	Galr3
-Gal	Galr1
-Gal	Galr2
-Gal	Galr3
-Gas6	Axl
-Gas6	Mertk
-Gas6	Tyro3
-Gast	Cckbr
-Gcg	Gcgr
-Gcg	Glp1r
-Gcg	Glp2r
-Gdf11	Acvr1b
-Gdf11	Acvr2a
-Gdf11	Acvr2b
-Gdf2	Acvrl1
-Gdf5	Bmpr1b
-Gdf5	Bmpr2
-Gdf5	Ror2
-Gdf6	Bmpr1a
-Gdf6	Bmpr2
-Gdf7	Acvr2a
-Gdf7	Bmpr1a
-Gdf7	Bmpr2
-Gdf9	Bmpr2
-Gdf9	Tgfbr1
-Gdnf	Gfra1
-Gdnf	Gfra2
-Gdnf	Ret
-Gh1	Ghr
-Gh2	Ghr
-Ghrh	Ghrhr
-Ghrh	Vipr1
-Ghrl	Ghsr
-Ghrl	Gpr39
-Gip	Gipr
-Gnrh1	Gnrhr
-Gnrh2	Gnrhr
-Gpha2	Tshr
-Gpi	Amfr
-Grp	Grpr
-Gstp1	Traf2
-Guca2a	Gucy2c
-Guca2b	Gucy2c
-Gzmb	Igf2r
-Has2	Cd44
-Has2	Hmmr
-Hbegf	Egfr
-Hbegf	Erbb4
-Hcrt	Hcrtr1
-Hcrt	Hcrtr2
-Hebp1	Fpr3
-Hgf	Met
-Hla-a	Kir3dl2
-Hla-b	Kir3dl1
-Hla-c	Kir2dl1
-Hla-c	Kir2dl3
-Hla-c	Kir2ds4
-Hla-e	Klrc1
-Hla-e	Klrc2
-Hla-e	Klrd1
-Hla-g	Kir2dl4
-Hla-g	Klrc1
-Hla-g	Klrd1
-Hla-g	Lilrb1
-Hspg2	Ptprs
-Iapp	Calcr
-Icam1	Itgal
-Icam1	Itgax
-Icam1	Itgb2
-Icam2	Itgal
-Icam2	Itgb2
-Icam3	Itgal
-Icam3	Itgb2
-Icam4	Itga2b
-Icam4	Itgal
-Icam4	Itgam
-Icam4	Itgav
-Icam4	Itgb2
-Icam4	Itgb3
-Icam5	Itgal
-Icam5	Itgb2
-Ifna10	Ifnar1
-Ifna10	Ifnar2
-Ifna13	Ifnar1
-Ifna13	Ifnar2
-Ifna14	Ifnar1
-Ifna14	Ifnar2
-Ifna16	Ifnar1
-Ifna16	Ifnar2
-Ifna17	Ifnar1
-Ifna17	Ifnar2
-Ifna1	Ifnar1
-Ifna1	Ifnar2
-Ifna21	Ifnar1
-Ifna21	Ifnar2
-Ifna2	Ifnar1
-Ifna2	Ifnar2
-Ifna4	Ifnar1
-Ifna4	Ifnar2
-Ifna5	Ifnar1
-Ifna5	Ifnar2
-Ifna6	Ifnar1
-Ifna6	Ifnar2
-Ifna7	Ifnar1
-Ifna7	Ifnar2
-Ifna8	Ifnar1
-Ifna8	Ifnar2
-Ifnb1	Ifnar1
-Ifnb1	Ifnar2
-Ifng	Ifngr1
-Ifng	Ifngr2
-Ifnl1	Ifnlr1
-Ifnl1	Il10rb
-Ifnl2	Ifnlr1
-Ifnl2	Il10rb
-Ifnl3	Ifnlr1
-Ifnl3	Il10rb
-Ifnw1	Ifnar1
-Ifnw1	Ifnar2
-Igf1	Igf1r
-Igf2	Igf1r
-Igf2	Igf2r
-Igf2	Insr
-Ihh	Hhip
-Ihh	Ptch1
-Il10	Il10ra
-Il10	Il10rb
-Il11	Il11ra
-Il11	Il6st
-Il12a	Il12rb1
-Il12a	Il12rb2
-Il12b	Il12rb1
-Il12b	Il12rb2
-Il13	Il13ra1
-Il13	Il13ra2
-Il13	Il2rg
-Il13	Il4r
-Il15	Il15ra
-Il15	Il2rb
-Il15	Il2rg
-Il16	Cd4
-Il17a	Il17ra
-Il17b	Il17rb
-Il18	Il18r1
-Il18	Il18rap
-Il18	Il1rapl1
-Il19	Il20ra
-Il19	Il20rb
-Il1a	Il1r1
-Il1a	Il1r2
-Il1b	Il1r1
-Il1b	Il1r2
-Il1b	Il1rap
-Il1rn	Il1r1
-Il1rn	Il1r2
-Il20	Il20ra
-Il20	Il20rb
-Il20	Il22ra1
-Il21	Il21r
-Il21	Il2rg
-Il22	Il10ra
-Il22	Il22ra1
-Il22	Il22ra2
-Il23a	Il12rb1
-Il23a	Il23r
-Il24	Il20ra
-Il24	Il20rb
-Il24	Il22ra1
-Il25	Il17rb
-Il2	Il2ra
-Il2	Il2rb
-Il2	Il2rg
-Il31	Il31ra
-Il31	Osmr
-Il3	Csf2rb
-Il3	Il3ra
-Il4	Il13ra1
-Il4	Il2rg
-Il4	Il4r
-Il5	Csf2rb
-Il5	Il5ra
-Il6	Il6r
-Il6	Il6st
-Il7	Il2rg
-Il7	Il7r
-Il8	Cxcr1
-Il8	Cxcr2
-Il8	Darc
-Il9	Il2rg
-Il9	Il9r
-Inha	Acvr2a
-Inha	Tgfbr3
-Inhba	Acvr1
-Inhba	Acvr1b
-Inhba	Acvr2a
-Inhba	Acvr2b
-Inhba	Bambi
-Inhbb	Acvr1
-Inhbb	Acvr1b
-Inhbb	Acvr2a
-Inhbb	Acvr2b
-Inhbc	Acvr1
-Inhbc	Acvr1b
-Inhbc	Acvr2a
-Inhbc	Acvr2b
-Insl3	Rxfp2
-Insl5	Rxfp3
-Insl5	Rxfp4
-Ins	Insr
-Jag1	Notch1
-Jag1	Notch2
-Jag1	Notch3
-Jag1	Notch4
-Jag2	Notch1
-Jag2	Notch2
-Jag2	Notch3
-Kiss1	Kiss1r
-Kitlg	Kit
-Kng1	Bdkrb1
-Kng1	Bdkrb2
-Kng1	Gpr135
-Lama1	Itga7
-Lama1	Itgb1
-Lama1	Itgb8
-Lama1	Rpsa
-Lama2	Itga7
-Lama2	Itgb1
-Lama2	Rpsa
-Lamb1	Itga6
-Lamb1	Itgb1
-Lamb2	Rpsa
-Lamc2	Itga3
-Lamc2	Itga6
-Lamc2	Itgb1
-Lamc2	Itgb4
-Lefty2	Acvr2b
-Lep	Lepr
-Lhb	Lhcgr
-Lif	Il6st
-Lif	Lifr
-Liph	Lpar1
-Liph	Lpar2
-Liph	Lpar4
-Lrpap1	Lrp1
-Lta	Ltbr
-Lta	Tnfrsf14
-Lta	Tnfrsf1a
-Lta	Tnfrsf1b
-Ltb	Cd40
-Ltb	Ltbr
-Ltf	Lrp1
-Ltf	Lrp11
-Madcam1	Itga4
-Madcam1	Itgb7
-Mdk	Alk
-Mdk	Ptprz1
-Mln	Mlnr
-Mmp13	Lrp1
-Mmp9	Lrp1
-Mst1	Mst1r
-Nampt	Insr
-Ncam1	Robo1
-Ncam1	Robo3
-Ndp	Fzd4
-Ndp	Lgr4
-Ngf	Ngfr
-Ngf	Ntrk1
-Ngf	Sort1
-Nid1	Ptprf
-Nlgn1	Nrxn1
-Nlgn1	Nrxn3
-Nlgn2	Nrxn1
-Nlgn2	Nrxn2
-Nlgn2	Nrxn3
-Nlgn3	Nrxn1
-Nlgn3	Nrxn2
-Nlgn3	Nrxn3
-Nmb	Grpr
-Nmb	Nmbr
-Nms	Nmur1
-Nms	Nmur2
-Nmu	Nmur1
-Nmu	Nmur2
-Nodal	Acvr1b
-Nodal	Acvr1c
-Nodal	Acvr2a
-Nodal	Acvr2b
-Nov	Notch1
-Npb	Npbwr1
-Npb	Npbwr2
-Npff	Npffr1
-Npff	Npffr2
-Npnt	Itga8
-Npnt	Itgb1
-Nppa	Npr1
-Nppa	Npr3
-Nppb	Npr1
-Nppb	Npr2
-Nppb	Npr3
-Nppc	Npr2
-Nps	Npsr1
-Npvf	Npffr1
-Npvf	Npffr2
-Npw	Npbwr1
-Npw	Npbwr2
-Npy	Npy1r
-Npy	Npy2r
-Npy	Npy4r
-Npy	Npy5r
-Npy	Prlhr
-Nrg1	Erbb2
-Nrg1	Erbb3
-Nrg1	Erbb4
-Nrg2	Erbb3
-Nrg2	Erbb4
-Nrg3	Erbb4
-Nrg4	Erbb4
-Nrtn	Gfra1
-Nrtn	Gfra2
-Nrtn	Ret
-Ntf3	Ngfr
-Ntf3	Ntrk1
-Ntf3	Ntrk2
-Ntf3	Ntrk3
-Ntf4	Ngfr
-Ntf4	Ngfrap1
-Ntf4	Ntrk1
-Ntf4	Ntrk2
-Ntn1	Dcc
-Ntn1	Unc5c
-Ntn3	Cdon
-Ntn3	Neo1
-Ntn4	Dcc
-Ntn4	Unc5a
-Ntng1	Lrrc4c
-Nts	Ntsr1
-Nts	Ntsr2
-Nxph1	Nrxn1
-Nxph1	Nrxn2
-Nxph1	Nrxn3
-Nxph3	Nrxn1
-Nxph3	Nrxn2
-Nxph3	Nrxn3
-Omg	Lingo1
-Omg	Tnfrsf1b
-Osm	Il6st
-Osm	Lifr
-Osm	Osmr
-Ostn	Npr3
-Oxt	Avpr1a
-Oxt	Avpr1b
-Oxt	Avpr2
-Oxt	Oxtr
-Pdgfa	Pdgfra
-Pdgfb	Pdgfra
-Pdgfb	Pdgfrb
-Pdgfc	Flt4
-Pdgfc	Kdr
-Pdgfc	Pdgfra
-Pdgfd	Pdgfrb
-Pdyn	Oprd1
-Pdyn	Oprk1
-Pdyn	Oprm1
-Penk	Mrgprx1
-Penk	Ogfr
-Penk	Oprd1
-Penk	Oprm1
-Pf4	Fgfr2
-Pf4	Ldlr
-Pf4	Procr
-Pf4	Thbd
-Pgf	Flt1
-Pgf	Nrp1
-Plat	Lrp1
-Plau	Lrp1
-Plau	Plaur
-Plg	Itga9
-Plg	Itgb1
-Pmch	Mchr1
-Pmch	Mchr2
-Pnoc	Oprl1
-Podxl2	Sell
-Pomc	Mc1r
-Pomc	Mc2r
-Pomc	Mc3r
-Pomc	Mc4r
-Pomc	Mc5r
-Pomc	Oprd1
-Pomc	Oprk1
-Pomc	Oprm1
-Ppbp	Cxcr1
-Ppbp	Cxcr2
-Ppy	Npy4r
-Ppy	Npy5r
-Prlh	Prlhr
-Prl	Prlr
-Prnd	Rpsa
-Proc	Procr
-Prok1	Prokr1
-Prok1	Prokr2
-Prok2	Prokr1
-Prok2	Prokr2
-Pros1	Axl
-Pros1	Tyro3
-Psap	Gpr37
-Psap	Gpr37l1
-Psap	Lrp1
-Psen1	Ncstn
-Pspn	Gfra4
-Pspn	Ret
-Ptdss1	Jmjd6
-Ptdss1	Scarb1
-Ptgs2	Ptgdr2
-Pth2	Pth1r
-Pth2	Pth2r
-Pthlh	Prlhr
-Pthlh	Pth1r
-Pthlh	Pth2r
-Pth	Pth1r
-Pth	Pth2r
-Ptn	Ptprb
-Ptn	Ptprz1
-Pyy	Npy1r
-Pyy	Npy2r
-Pyy	Npy4r
-Pyy	Npy5r
-Qrfp	P2ry14
-Qrfp	Qrfpr
-Rarres2	Cmklr1
-Rarres2	Gpr1
-Reln	Itga3
-Reln	Itgb1
-Reln	Lrp8
-Reln	Vldlr
-Ren	Atp6ap2
-Rgma	Neo1
-Rln1	Rxfp1
-Rln1	Rxfp2
-Rln2	Rxfp1
-Rln2	Rxfp2
-Rln3	Rxfp1
-Rln3	Rxfp2
-Rln3	Rxfp3
-Rln3	Rxfp4
-Rps19	C5ar1
-Rspo1	Lgr4
-Rspo1	Lgr5
-Rspo1	Lgr6
-Rspo1	Lrp6
-Rspo2	Lgr4
-Rspo2	Lgr5
-Rspo2	Lgr6
-Rspo3	Lgr4
-Rspo3	Lgr5
-Rspo3	Lgr6
-Rspo4	Lgr4
-Rspo4	Lgr5
-Rspo4	Lgr6
-Rtn4	Lingo1
-Rtn4	Rtn4r
-Rtn4	Tnfrsf19
-Saa1	Fpr2
-Sct	Sctr
-Selplg	Sele
-Selplg	Selp
-Sema3a	Nrp1
-Sema3a	Plxna1
-Sema3a	Plxna2
-Sema3a	Plxna4
-Sema3b	Nrp1
-Sema3c	Nrp2
-Sema3e	Plxnd1
-Sema3f	Nrp2
-Sema3f	Plxna3
-Sema4d	Met
-Sema4d	Plxnb1
-Sema4d	Plxnb2
-Sema5a	Met
-Sema5a	Plxnb3
-Sema6d	Kdr
-Sema6d	Plxna1
-Sema7a	Plxnc1
-Serpina1	Lrp1
-Serpinc1	Lrp1
-Serpine1	Lrp1
-Serpine2	Lrp1
-Serping1	Lrp1
-Shank1	Lphn1
-Shh	Boc
-Shh	Cdon
-Shh	Hhip
-Shh	Ptch1
-Shh	Smo
-Slit1	Gpc1
-Slit1	Robo1
-Slit1	Sdc1
-Slit2	Gpc1
-Slit2	Robo1
-Slit2	Robo2
-Slit2	Robo4
-Slit2	Sdc1
-Sost	Lrp5
-Sost	Lrp6
-Spp1	Cd44
-Spp1	Itgav
-Sst	Sstr1
-Sst	Sstr2
-Sst	Sstr3
-Sst	Sstr4
-Sst	Sstr5
-Tac1	Tacr1
-Tac1	Tacr2
-Tac1	Tacr3
-Tac3	Tacr1
-Tac3	Tacr2
-Tac3	Tacr3
-Tac4	Tacr1
-Tac4	Tacr3
-Tdgf1	Acvr2a
-Tfpi	Lrp1
-Tfpi	Vldlr
-Tf	Tfrc
-Tgfa	Egfr
-Tgfb1	Acvrl1
-Tgfb1	Tgfbr1
-Tgfb1	Tgfbr2
-Tgfb1	Tgfbr3
-Tgfb2	Tgfbr1
-Tgfb2	Tgfbr2
-Tgfb2	Tgfbr3
-Tgfb3	Acvrl1
-Tgfb3	Tgfbr1
-Tgfb3	Tgfbr2
-Tgfb3	Tgfbr3
-Tgm2	Gpr56
-Thbs1	Cd36
-Thbs1	Cd47
-Thbs1	Sdc1
-Thbs2	Cd47
-Thpo	Mpl
-Tnfsf10	Tnfrsf10a
-Tnfsf10	Tnfrsf10b
-Tnfsf10	Tnfrsf10c
-Tnfsf10	Tnfrsf10d
-Tnfsf10	Tnfrsf11b
-Tnfsf11	Tnfrsf11a
-Tnfsf11	Tnfrsf11b
-Tnfsf12	Tnfrsf12a
-Tnfsf12	Tnfrsf25
-Tnfsf13b	Tnfrsf13b
-Tnfsf13b	Tnfrsf13c
-Tnfsf13b	Tnfrsf17
-Tnfsf13	Tnfrsf13b
-Tnfsf13	Tnfrsf17
-Tnfsf14	Ltbr
-Tnfsf14	Tnfrsf14
-Tnfsf14	Tnfrsf6b
-Tnfsf15	Tnfrsf25
-Tnfsf18	Tnfrsf18
-Tnfsf4	Tnfrsf4
-Tnfsf8	Tnfrsf8
-Tnfsf9	Tnfrsf9
-Tnf	Tnfrsf1a
-Tnf	Tnfrsf1b
-Tnf	Tnfrsf21
-Trh	Trhr
-Tshb	Tshr
-Ucn2	Crhr1
-Ucn2	Crhr2
-Ucn3	Crhr2
-Ucn	Crhr1
-Ucn	Crhr2
-Ulbp2	Klrk1
-Uts2b	Uts2r
-Uts2	Uts2r
-Vcam1	Itga4
-Vcam1	Itgad
-Vcam1	Itgb1
-Vcam1	Itgb2
-Vegfa	Flt1
-Vegfa	Kdr
-Vegfa	Nrp1
-Vegfa	Nrp2
-Vegfb	Flt1
-Vegfb	Nrp1
-Vegfc	Flt4
-Vegfc	Kdr
-Vegfc	Nrp2
-Vegfc	Vipr2
-Vip	Adcyap1r1
-Vip	Sctr
-Vip	Vipr1
-Vip	Vipr2
-Vtn	Itga5
-Vtn	Itgb3
-Wnt11	Fzd7
-Wnt1	Fzd3
-Wnt1	Fzd8
-Wnt1	Fzd9
-Wnt1	Ryk
-Wnt3a	Fzd6
-Wnt3	Fzd8
-Wnt3	Lrp6
-Wnt3	Ryk
-Wnt4	Fzd2
-Wnt4	Fzd6
-Wnt5a	Fzd2
-Wnt5a	Fzd4
-Wnt5a	Fzd6
-Wnt5a	Fzd7
-Wnt5a	Ryk
-Wnt7a	Fzd5
-Wnt7b	Fzd1
-Wnt7b	Fzd10
-Wnt7b	Lrp5
-Xcl1	Xcr1
-Xcl2	Xcr1
-Yars	Cxcr1
-Zp3	Mertk
diff --git a/inst/extdata/sig_matrix.txt b/inst/extdata/sig_matrix.txt
deleted file mode 100644
index 3bbbcebf3..000000000
--- a/inst/extdata/sig_matrix.txt
+++ /dev/null
@@ -1,875 +0,0 @@
-Event	Astro_ependymal	Cerebellum	Cholinergic_monoaminergic	Cortex_hippocampus_thalamus	Cortex_hippocampus	di_mesencephalon_1	di_mesencephalon_2	Ensheathing_satelliteGlia	Granule_neurons	Hindbrain	Immune	Medium_spiny_neurons	Neuroblasts_1	Neuroblasts_2	Olfactory_bulb	Oligo_dendrocyte	Peptidergic	Spinal_cord_1	Spinal_cord_2	Vascular
-Cartpt	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Gm15469	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Pmch	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Ly6a	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
-Fibcd1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
-Slc6a5	0	1	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
-Fam183b	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-Nts	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0
-Syce2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
-Cox6a2	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-5031425F14Rik	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Gata3	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0
-6330403A02Rik	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Cited1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-Skor1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
-Pbx3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
-Ccdc80	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
-Fam159b	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
-Nr3c2	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-Cdca7	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
-Krt15	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Cidea	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Lhx6	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Cbln3	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Pgr15l	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Hoxb6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0
-Hoxb2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0
-Scn1a	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Tekt5	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Lypd6b	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Ucma	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
-Parm1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Penk	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
-Apoc1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Mia	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Wipf3	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Drd5	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-1110032F04Rik	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Igsf1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Efhd1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-Tfap2b	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0
-Lgals9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
-Zic1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
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diff --git a/vignettes/.gitignore b/vignettes/.gitignore
deleted file mode 100644
index 097b24163..000000000
--- a/vignettes/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*.html
-*.R