Runs the Slingshot algorithm on a Seurat object.
Usage
RunSlingshot(
srt,
group.by,
reduction = NULL,
dims = NULL,
start = NULL,
end = NULL,
prefix = NULL,
reverse = FALSE,
align_start = FALSE,
show_plot = TRUE,
lineage_palette = "Dark2",
seed = 11,
...
)Arguments
- srt
A Seurat object.
- group.by
The variable to group the cells by.
- reduction
The reduction technique to use for dimensionality reduction. Default is NULL, which uses the default reduction for the Seurat object.
- dims
The dimensions to use for the Slingshot algorithm. Default is NULL, which uses first two dimensions.
- start
The starting group for the Slingshot algorithm. Default is NULL.
- end
The ending group for the Slingshot algorithm. Default is NULL.
- prefix
The prefix to add to the column names of the resulting pseudotime variable. Default is NULL.
- reverse
Logical value indicating whether to reverse the pseudotime variable. Default is FALSE.
- align_start
Logical value indicating whether to align the starting pseudotime values at the maximum pseudotime. Default is FALSE.
- show_plot
Logical value indicating whether to show the dimensionality plot. Default is TRUE.
- lineage_palette
The color palette to use for the lineages in the plot. Default is "Dark2".
- seed
The random seed to use for reproducibility. Default is 11.
- ...
Additional arguments to be passed to the slingshot::slingshot function.
Examples
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2025-09-20 13:58:26] Start standard scop workflow...
#> ℹ [2025-09-20 13:58:27] Checking a list of <Seurat> object...
#> ! [2025-09-20 13:58:27] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2025-09-20 13:58:27] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on the data 1/1 of the `srt_list`...
#> ℹ [2025-09-20 13:58:29] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2025-09-20 13:58:29] Use the separate HVF from srt_list
#> ℹ [2025-09-20 13:58:29] Number of available HVF: 2000
#> ℹ [2025-09-20 13:58:30] Finished check
#> ℹ [2025-09-20 13:58:30] Perform `Seurat::ScaleData()`
#> Warning: Different features in new layer data than already exists for scale.data
#> ℹ [2025-09-20 13:58:30] Perform pca linear dimension reduction
#> StandardPC_ 1
#> Positive: Aplp1, Cpe, Gnas, Fam183b, Map1b, Hmgn3, Pcsk1n, Chga, Tuba1a, Bex2
#> Syt13, Isl1, 1700086L19Rik, Pax6, Chgb, Scgn, Rbp4, Scg3, Gch1, Camk2n1
#> Cryba2, Pcsk2, Pyy, Tspan7, Mafb, Hist3h2ba, Dbpht2, Abcc8, Rap1b, Slc38a5
#> Negative: Spp1, Anxa2, Sparc, Dbi, 1700011H14Rik, Wfdc2, Gsta3, Adamts1, Clu, Mgst1
#> Bicc1, Ldha, Vim, Cldn3, Cyr61, Rps2, Mt1, Ptn, Phgdh, Nudt19
#> Smtnl2, Smco4, Habp2, Mt2, Col18a1, Rpl12, Galk1, Cldn10, Acot1, Ccnd1
#> StandardPC_ 2
#> Positive: Rbp4, Tagln2, Tuba1b, Fkbp2, Pyy, Pcsk2, Iapp, Tmem27, Meis2, Tubb4b
#> Pcsk1n, Dbpht2, Rap1b, Dynll1, Tubb2a, Sdf2l1, Scgn, 1700086L19Rik, Scg2, Abcc8
#> Atp1b1, Hspa5, Fam183b, Papss2, Slc38a5, Scg3, Mageh1, Tspan7, Ppp1r1a, Ociad2
#> Negative: Neurog3, Btbd17, Gadd45a, Ppp1r14a, Neurod2, Sox4, Smarcd2, Mdk, Pax4, Btg2
#> Sult2b1, Hes6, Grasp, Igfbpl1, Gpx2, Cbfa2t3, Foxa3, Shf, Mfng, Tmsb4x
#> Amotl2, Gdpd1, Cdc14b, Epb42, Rcor2, Cotl1, Upk3bl, Rbfox3, Cldn6, Cer1
#> StandardPC_ 3
#> Positive: Nusap1, Top2a, Birc5, Aurkb, Cdca8, Pbk, Mki67, Tpx2, Plk1, Ccnb1
#> 2810417H13Rik, Incenp, Cenpf, Ccna2, Prc1, Racgap1, Cdk1, Aurka, Cdca3, Hmmr
#> Spc24, Kif23, Sgol1, Cenpe, Cdc20, Hist1h1b, Cdca2, Mxd3, Kif22, Ska1
#> Negative: Anxa5, Pdzk1ip1, Acot1, Tpm1, Anxa2, Dcdc2a, Capg, Sparc, Ttr, Pamr1
#> Clu, Cxcl12, Ndrg2, Hnf1aos1, Gas6, Gsta3, Krt18, Ces1d, Atp1b1, Muc1
#> Hhex, Acadm, Spp1, Enpp2, Bcl2l14, Sat1, Smtnl2, 1700011H14Rik, Tgm2, Fam159a
#> StandardPC_ 4
#> Positive: Glud1, Tm4sf4, Akr1c19, Cldn4, Runx1t1, Fev, Pou3f4, Gm43861, Pgrmc1, Arx
#> Cd200, Lrpprc, Hmgn3, Ppp1r14c, Pam, Etv1, Tsc22d1, Slc25a5, Akap17b, Pgf
#> Fam43a, Emb, Jun, Krt8, Dnajc12, Mid1ip1, Ids, Rgs17, Uchl1, Alcam
#> Negative: Ins2, Ins1, Ppp1r1a, Nnat, Calr, Sytl4, Sdf2l1, Iapp, Pdia6, Mapt
#> G6pc2, C2cd4b, Npy, Gng12, P2ry1, Ero1lb, Adra2a, Papss2, Arhgap36, Fam151a
#> Dlk1, Creld2, Gip, Tmem215, Gm27033, Cntfr, Prss53, C2cd4a, Lyve1, Ociad2
#> StandardPC_ 5
#> Positive: Pdx1, Nkx6-1, Npepl1, Cldn4, Cryba2, Fev, Jun, Chgb, Gng12, Adra2a
#> Mnx1, Sytl4, Pdk3, Gm27033, Nnat, Chga, Ins2, 1110012L19Rik, Enho, Krt7
#> Mlxipl, Tmsb10, Flrt1, Pax4, Tubb3, Prrg2, Gars, Frzb, BC023829, Gm2694
#> Negative: Irx2, Irx1, Gcg, Ctxn2, Tmem27, Ctsz, Tmsb15l, Nap1l5, Pou6f2, Gria2
#> Ghrl, Peg10, Smarca1, Arx, Lrpap1, Rgs4, Ttr, Gast, Tmsb15b2, Serpina1b
#> Slc16a10, Wnk3, Ly6e, Auts2, Sct, Arg1, Dusp10, Sphkap, Dock11, Edn3
#> ℹ [2025-09-20 13:58:31] Perform `Seurat::FindClusters()` with louvain and `cluster_resolution` = 0.6
#> ℹ [2025-09-20 13:58:31] Reorder clusters...
#> ! [2025-09-20 13:58:31] Using `Seurat::AggregateExpression()` to calculate pseudo-bulk data for <Assay5>
#> ℹ [2025-09-20 13:58:31] Perform umap nonlinear dimension reduction
#> ℹ [2025-09-20 13:58:31] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-09-20 13:58:31] UMAP will return its model
#> ℹ [2025-09-20 13:58:36] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-09-20 13:58:36] UMAP will return its model
#> ✔ [2025-09-20 13:58:40] Run scop standard workflow done
pancreas_sub <- RunSlingshot(
pancreas_sub,
group.by = "SubCellType",
reduction = "UMAP"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_path()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_path()`).
pancreas_sub <- RunSlingshot(
pancreas_sub,
group.by = "SubCellType",
reduction = "PCA",
dims = 1:10
)
#> Error in (function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "subscript out of bounds", call = srt_sub[[reduction]]@cell.embeddings[, dims], object = structure(c(6.83167837844486, -1.89048684849148, 5.98617838607426, -3.88185669197445, -3.84871317161922, 5.60678242431278, -3.84207726730709, -3.7566142202795, -4.08858896507626, -2.33485282673244, 6.70149420486088, -3.33260060562496, -4.07526494278316, -6.659483921665, -1.41885952367191, -1.73217345489864, -6.76706649078731, -2.596460235256, 1.07538651214237, -0.637805771964835, -2.88553704037075, 5.81642817245121, 2.67789386497135, 5.14438627944584, -0.623891335862921, 6.78055952773686, -4.66297770752315, 7.10836361632938, -3.38915253891353, 5.70976017699833, 5.8407487748682, 2.64417623267765, 6.71542643294926, 6.59851931319828, -5.75813771499996, -6.88043357147579, -1.28520212783222, 6.70302771316166, 6.31364105926151, -1.62847281708126, -6.00797225250606, 5.48040817962284, 5.91766213164921, 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1.878351491048, -0.976080376551486, 0.294399242951535, 2.98534635837283, -3.75359149639402, 1.40337900455203, -2.86797686283384, 0.433541219784878, -3.55430360500608, 0.138601582600735, -2.68958135311399, -3.02842565243039, 1.01208321387973, -2.00057919685636, -4.0112695283154, 1.54594568546023, 4.45689467723574, 0.189439904048108, -2.93067403499875, -3.68703718845639, -2.7714447564343, 2.08969120319095, 1.56206242377963, 1.50641838844027, 2.53560356433596, -0.441304135964252, -2.50188513462339, 2.99446801479068, -2.86030026142392, -4.07937689487729, 3.02802972133365, 1.67129592235293, 3.03864173228946, 0.624103766038083 ), dim = c(1000L, 2L), "`scaled:center`" = c(1.11974288238888, 0.187784392283298), dimnames = list(c("AAACCTGAGCCTTGAT", "AAACCTGGTAAGTGGC", "AAACGGGAGATATGGT", "AAACGGGCAAAGAATC", "AAACGGGGTACAGTTC", "AAACGGGTCAGCTCTC", "AAACGGGTCGCATGGC", "AAAGATGAGTCATGCT", "AAAGATGAGTCTTGCA", "AAAGCAAAGCTACCTA", "AAAGCAACACATGGGA", "AAAGCAAGTGCAGTAG", "AAATGCCAGACTAAGT", "AAATGCCCAATGGAAT", "AAATGCCCACCAACCG", "AAATGCCCATGCTAGT", "AAATGCCGTGATAAGT", "AACACGTGTCGACTGC", "AACCATGCACAGGAGT", "AACCATGGTTCGGCAC", "AACCATGGTTGAACTC", "AACGTTGGTGCCTTGG", "AACTCAGGTGCCTGTG", "AACTCAGGTTGGAGGT", "AACTCAGTCCTCGCAT", "AACTCAGTCTGGTTCC", "AACTCCCCAGTTCATG", "AACTCCCTCGAGAGCA", "AACTCTTCATTTGCCC", "AACTGGTGTGCCTGTG", "AACTGGTTCTTACCGC", "AACTTTCCACAGTCGC", "AACTTTCCACTGCCAG", "AACTTTCGTGACCAAG", "AACTTTCTCCAGATCA", "AAGACCTAGACCTTTG", "AAGACCTAGTAGGCCA", "AAGACCTCAGGTTTCA", "AAGCCGCAGGCAGGTT", "AAGCCGCCAATGGACG", "AAGGAGCAGTACATGA", "AAGGCAGAGCTGAAAT", "AAGGCAGTCCGAGCCA", "AAGGTTCAGATAGTCA", "AAGGTTCAGGAGCGAG", "AAGGTTCGTCAACTGT", "AAGTCTGGTTGGGACA", "AAGTCTGTCCGAGCCA", "AATCCAGAGGGTTCCC", "AATCCAGTCAGGTTCA", "AATCCAGTCGGTCCGA", "AATCGGTCATATGGTC", "AATCGGTTCCAAACTG", "AATCGGTTCGTATCAG", "ACACCAAGTATAGGTA", "ACACCCTAGGACAGCT", "ACACCCTTCCCAGGTG", "ACACCGGCATCACGTA", "ACACCGGCATGTCCTC", "ACACCGGTCATGTCTT", "ACACTGAGTCCATGAT", "ACAGCCGAGAGAACAG", "ACAGCCGAGAGGTACC", "ACAGCCGAGTGGTCCC", "ACAGCCGCATCGTCGG", "ACAGCTAAGTCGTTTG", "ACAGCTATCAAGGCTT", "ACAGCTATCAGCATGT", "ACAGCTATCTGGGCCA", "ACATACGAGTAGGCCA", "ACATACGGTCTCTCTG", "ACATCAGAGAGACTTA", "ACATCAGTCCTTGGTC", "ACCAGTAAGTGATCGG", "ACCAGTAGTTCGTTGA", "ACCAGTATCGTTTAGG", "ACCGTAAGTTATCACG", "ACCTTTATCCTGCAGG", "ACGAGCCCATGAGCGA", "ACGAGGAAGTTACCCA", "ACGAGGATCATCACCC", "ACGAGGATCGCCGTGA", "ACGATACAGATGAGAG", "ACGATACTCGCGCCAA", "ACGATGTTCGCAGGCT", "ACGCAGCCATTCTCAT", "ACGCAGCGTAATCACC", "ACGCCAGGTTACAGAA", "ACGCCAGTCCCAAGTA", "ACGCCGAAGGGTGTTG", "ACGCCGAGTTTGCATG", "ACGGCCACACGTGAGA", "ACGGGCTGTGCGATAG", "ACGTCAAAGGTGTTAA", "ACGTCAACACTGCCAG", "ACGTCAACAGACAAAT", "ACTATCTGTCAGGACA", "ACTATCTTCAAGATCC", "ACTGAACAGCCTCGTG", "ACTGAGTAGTGACTCT", "ACTGATGCATCAGTAC", "ACTGATGCATGGTCTA", "ACTGATGCATGTCTCC", "ACTGATGGTGAGGGTT", "ACTGATGTCCCTAACC", "ACTGCTCAGGTGTTAA", "ACTGTCCCAGTTTACG", "ACTGTCCTCGCTAGCG", "ACTTACTAGAGGGCTT", "ACTTACTAGCCGGTAA", "ACTTACTCAATCAGAA", "ACTTACTCACATGTGT", "ACTTGTTAGTGAAGTT", "ACTTGTTAGTTAAGTG", "ACTTGTTCATGGTCAT", "ACTTGTTTCACCCGAG", "ACTTTCAAGGATATAC", "ACTTTCACAACTGCTA", "AGAATAGCAATCACAC", "AGAATAGCAGTACACT", "AGACGTTCAATGGTCT", "AGACGTTTCTTACCTA", "AGAGCGACAGTAAGAT", "AGAGCGATCTCTTGAT", "AGAGCTTAGCCGATTT", "AGAGCTTAGGTTACCT", "AGAGCTTGTTAAAGAC", "AGAGTGGAGGCGATAC", "AGAGTGGCACCTCGGA", "AGAGTGGGTAGCACGA", "AGAGTGGGTCACCTAA", "AGATCTGTCCGTCAAA", "AGATTGCAGCGTGTCC", "AGATTGCAGCTGTCTA", "AGATTGCAGTTCCACA", "AGATTGCCACCAGGCT", "AGCAGCCGTCGCATCG", "AGCAGCCGTGTAACGG", "AGCAGCCTCTTTAGTC", "AGCATACCACAGCCCA", "AGCATACGTCCGCTGA", "AGCGGTCGTACCGAGA", "AGCGGTCGTCGAATCT", "AGCGGTCGTGTATGGG", "AGCGTCGCACAGGCCT", "AGCTCCTCAGTTTACG", "AGCTCCTGTGTGCCTG", "AGCTCCTTCAATACCG", "AGCTCCTTCGCCCTTA", "AGCTCTCAGACATAAC", "AGCTCTCGTTCAGTAC", "AGCTTGAAGACACGAC", "AGCTTGAAGAGTGACC", "AGCTTGACAATAGAGT", "AGCTTGACAGTAAGAT", "AGCTTGACATCTATGG", "AGCTTGAGTGCAGTAG", "AGGCCACAGCTGTCTA", "AGGCCACCATGACATC", "AGGCCGTCACGACGAA", "AGGCCGTCACGGTGTC", "AGGCCGTGTACCAGTT", "AGGGAGTAGGGTATCG", "AGGGAGTAGTGTCTCA", "AGGGAGTTCCTCAATT", "AGGGAGTTCGGAGGTA", "AGGGATGGTCGACTGC", "AGGGATGGTTAGGGTG", "AGGGATGTCGCATGAT", "AGGGATGTCGCATGGC", "AGGGTGAGTGCGAAAC", "AGGTCATCACTTCTGC", "AGGTCATGTCTCCCTA", "AGGTCATGTTTAGGAA", "AGTAGTCCACATGACT", "AGTAGTCGTGAGGGAG", "AGTAGTCGTTCTGTTT", "AGTCTTTCACCAGGTC", "AGTCTTTCACGGACAA", "AGTCTTTGTTACGGAG", "AGTGAGGGTTACGGAG", "AGTGAGGTCTCCAACC", "AGTGGGACAGGTCGTC", "AGTGGGAGTGGCAAAC", "AGTGTCATCCCTTGTG", "AGTTGGTAGAGCCTAG", "AGTTGGTGTTGTCGCG", "AGTTGGTTCACATAGC", "ATAAGAGCATCGATTG", "ATAGACCAGCGTGTCC", "ATAGACCAGTGATCGG", "ATAGACCTCTAACTGG", "ATCACGAGTGCACCAC", "ATCATCTGTGTTTGTG", "ATCATCTTCTGTCAAG", "ATCATGGAGGAATGGA", "ATCATGGGTATTCGTG", "ATCATGGGTCCGCTGA", "ATCATGGTCCAGAGGA", "ATCCACCAGAGCCTAG", "ATCCACCCAGCTCGCA", "ATCCACCGTACCATCA", "ATCCGAAGTACACCGC", "ATCCGAAGTGACTCAT", "ATCTGCCCAATCCGAT", "ATCTGCCCATGTTGAC", "ATGAGGGTCTTGACGA", "ATGTGTGCACAAGTAA", "ATGTGTGTCAAAGACA", "ATTACTCAGTTGCAGG", "ATTACTCTCAGGCGAA", "ATTACTCTCTGCCAGG", "ATTATCCAGAAACCTA", "ATTATCCAGACCCACC", "ATTATCCAGTGAACAT", "ATTGGACAGTAATCCC", "ATTGGTGTCCAGTATG", "ATTTCTGGTAGTGAAT", "CAACCAAAGCGTTCCG", "CAACCAACAACCGCCA", "CAACCAACACCTCGTT", "CAACCAATCGGGAGTA", "CAAGAAAAGAGTACCG", "CAAGAAATCGTACCGG", "CAAGGCCAGCTGTTCA", "CAAGGCCAGTGTGGCA", "CAAGGCCCACATTTCT", "CAAGGCCTCAGTGCAT", "CAAGGCCTCTCAACTT", "CAAGGCCTCTTACCTA", "CAAGTTGGTGTGCCTG", "CAAGTTGTCTAACTGG", "CACAAACAGTAGCGGT", "CACAAACCACGAAAGC", "CACACAACAGCCAGAA", "CACACCTGTACATGTC", "CACACCTGTTATCCGA", "CACACTCAGATCCCAT", "CACACTCTCATGTGGT", "CACAGGCCAAGGCTCC", "CACAGGCCACGTCAGC", "CACAGTAGTGCACTTA", "CACAGTAGTTCCTCCA", "CACAGTATCCTCCTAG", "CACATAGAGCGTGTCC", "CACATTTGTTTCGCTC", "CACATTTTCGAGGTAG", "CACATTTTCGCAGGCT", "CACCACTAGCGATCCC", "CACCACTGTGTGTGCC", "CACCAGGCATAAAGGT", "CACCTTGAGAGTAATC", "CACTCCACATCGTCGG", "CACTCCATCAACACAC", "CAGAATCCATTGGGCC", "CAGAATCGTCATTAGC", "CAGAATCGTGTAAGTA", "CAGAGAGTCGGCCGAT", "CAGATCAAGCTGTTCA", "CAGCAGCAGACAAAGG", "CAGCAGCCACACTGCG", "CAGCAGCGTTCACGGC", "CAGCCGAAGCGATATA", "CAGCCGAAGTAGGTGC", "CAGCCGATCCTATTCA", "CAGCCGATCGTTTATC", "CAGCGACCACAGGAGT", "CAGCTAAAGTCCATAC", "CAGCTAACATGCCTAA", "CAGCTAAGTACCGAGA", "CAGCTGGCAAGTTGTC", "CAGCTGGGTCTAACGT", "CAGCTGGGTTCTCATT", "CAGGTGCAGCCAGGAT", "CAGGTGCCATCAGTCA", "CAGTCCTAGGTGGGTT", "CAGTCCTCAGGGCATA", "CATATGGCATGTTGAC", "CATATGGGTTACTGAC", "CATATGGTCACAGTAC", "CATATTCTCCTGTAGA", "CATCAGACATGCATGT", "CATCAGAGTCTCTTTA", "CATCAGATCATCGCTC", "CATCGAAGTACGAAAT", "CATCGAAGTCACACGC", "CATCGGGCACGTTGGC", "CATCGGGTCTTCGGTC", "CATGACACAACAACCT", "CATGACACATCGATTG", "CATGACAGTAGCTTGT", "CATGACATCATGCATG", "CATGCCTCACCCATTC", "CATGGCGAGAGTCTGG", "CATTATCGTCATATCG", "CCAATCCAGAGTAAGG", "CCACCTAAGACTTGAA", "CCACCTACAGCTCGAC", "CCACCTATCACCAGGC", "CCACCTATCTAAGCCA", "CCACGGAAGATCCTGT", "CCACGGAAGCAATCTC", "CCACGGAAGGGTGTTG", "CCACGGAAGTCTCCTC", "CCACGGAGTCAACATC", "CCACGGAGTCTAGTCA", "CCACGGAGTTACGACT", "CCACTACAGAGCTGGT", "CCACTACAGAGTACCG", "CCACTACCAACGCACC", "CCAGCGACAGACGTAG", "CCATGTCGTCGGCTCA", "CCATGTCTCCGCATAA", "CCATTCGCATGCCTAA", "CCATTCGGTAGGGACT", "CCCAATCCAACTGGCC", "CCCAGTTAGCATCATC", "CCCAGTTGTCGTGGCT", "CCCAGTTGTGCGCTTG", "CCCAGTTTCAGCACAT", "CCCATACAGACTTTCG", "CCCATACCACATCCAA", "CCCATACCATGCAACT", "CCCATACTCGTGGACC", "CCGGGATAGATCTGAA", "CCGGGATTCGACAGCC", "CCGGTAGTCGGCTTGG", "CCGTACTAGGAGTACC", "CCGTACTAGTCCGTAT", "CCGTACTTCAATAAGG", "CCGTGGACATAGAAAC", "CCGTGGATCCAAGCCG", "CCGTGGATCTGTCTCG", "CCGTGGATCTTAGAGC", "CCGTTCAAGCTAAACA", "CCGTTCAAGGACCACA", "CCGTTCACACATGACT", "CCTACACAGATCCGAG", "CCTACACAGTACGTTC", "CCTACACTCCTTTACA", "CCTACACTCTTTACAC", "CCTACCACATCGATTG", "CCTACCAGTTGCTCCT", "CCTACCATCTGCCCTA", "CCTAGCTCAGACTCGC", "CCTAGCTCATACTACG", "CCTAGCTGTGGCCCTA", "CCTAGCTTCGATGAGG", "CCTATTACAGACAAGC", "CCTATTATCATCGCTC", "CCTCAGTAGTGCGATG", "CCTCAGTCAGACACTT", "CCTCAGTGTTACCAGT", "CCTCTGAGTATAAACG", "CCTTACGAGATCACGG", "CCTTACGCACAACGCC", "CCTTCCCAGGCAGGTT", "CCTTCCCCAAAGTGCG", "CCTTCCCTCGTCGTTC", "CCTTCGAAGATAGCAT", "CCTTCGACAGCTGTTA", "CCTTCGATCACAGGCC", "CGAACATAGCCAGTAG", "CGAACATCAGACGTAG", "CGAATGTAGTTCCACA", "CGAATGTGTCTGGAGA", "CGAATGTTCACCGGGT", "CGAATGTTCTTCATGT", "CGACCTTAGCGCTTAT", "CGACCTTAGGCTAGAC", "CGACTTCCAGCCTATA", "CGACTTCCAGCTGCAC", "CGACTTCTCACGCGGT", "CGAGAAGAGGGTTCCC", "CGAGAAGCACGCATCG", "CGAGAAGTCGTTACAG", "CGAGCACAGCTGAAAT", "CGAGCACAGGCAGGTT", "CGAGCACGTAGTAGTA", "CGAGCACTCTACCTGC", "CGAGCACTCTTCGAGA", "CGATCGGAGCTGCAAG", "CGATCGGCACGCCAGT", "CGATGGCGTTACGGAG", "CGATGGCTCAGTGTTG", "CGATGGCTCTGTGCAA", "CGATGTAAGTTTAGGA", "CGATGTAGTACTCTCC", "CGATTGAAGTCAAGGC", "CGCCAAGCAAAGTCAA", "CGCCAAGCACCGGAAA", "CGCCAAGTCTAAGCCA", "CGCGGTAAGAGCTGGT", "CGCGGTAAGCTGCAAG", "CGCGTTTCAGTCTTCC", "CGCTGGAGTCCATCCT", "CGCTTCATCTCTGTCG", "CGGACACAGTGTCTCA", "CGGACGTAGACACGAC", "CGGACTGAGGTAGCTG", "CGGACTGTCTTGAGAC", "CGGAGCTAGATAGTCA", "CGGAGCTCATTGGGCC", "CGGAGTCAGTTTAGGA", "CGGCTAGGTACTCGCG", "CGGGTCAAGGCGATAC", "CGGGTCAAGGCTCAGA", "CGGTTAAAGAGCTGCA", "CGGTTAAGTAAACACA", "CGGTTAAGTCTAGCCG", "CGGTTAATCACCGGGT", "CGGTTAATCGTCTGAA", "CGTAGCGTCGGAAATA", "CGTAGGCAGCGTAGTG", "CGTCACTAGGGTGTGT", "CGTCACTCACGAAATA", "CGTCACTCATAGTAAG", "CGTCACTTCACTTATC", "CGTCACTTCTAACTCT", "CGTCAGGAGCCTATGT", "CGTCAGGCATGGGAAC", "CGTCAGGGTAGGCATG", "CGTCAGGTCCGCAAGC", "CGTCAGGTCCTGCCAT", "CGTCCATGTCTAACGT", "CGTCCATTCGCGCCAA", "CGTCTACAGATCTGCT", "CGTCTACAGGGAGTAA", "CGTGAGCTCAGCGATT", "CGTGAGCTCTTCTGGC", "CGTGTAAGTCTTGATG", "CGTGTAATCATTATCC", "CGTGTAATCCATGCTC", "CGTGTCTCAGAAGCAC", "CGTGTCTGTAGCGTCC", "CGTTAGAAGTATCTCG", "CGTTAGAGTGCAACGA", "CGTTCTGAGGACGAAA", "CGTTCTGTCACAATGC", "CGTTCTGTCGATAGAA", "CGTTGGGCAGGCGATA", "CTAACTTAGAGGTACC", "CTAACTTAGATCACGG", "CTAACTTCATCTGGTA", "CTAACTTCATTGGGCC", "CTAAGACAGCACGCCT", "CTAAGACAGCCACGCT", "CTAAGACGTATCAGTC", "CTAAGACTCTGCGGCA", "CTAATGGCATGGTTGT", "CTACACCCATCAGTCA", "CTACACCGTCGAATCT", "CTACACCGTCGCCATG", "CTACATTCACCGTTGG", "CTACATTGTTACTGAC", "CTACCCAGTGCGCTTG", "CTACGTCAGCTAGGCA", "CTAGAGTCACTGTTAG", "CTAGCCTGTCTCTTAT", "CTAGCCTGTTCGGGCT", "CTAGCCTTCAGCGATT", "CTAGTGATCAAAGACA", "CTAGTGATCCCAGGTG", "CTCACACGTCACACGC", "CTCAGAACACTAGTAC", "CTCAGAACATAGGATA", "CTCAGAAGTCCTCTTG", "CTCAGAATCAGGTTCA", "CTCATTACAAGCGCTC", "CTCCTAGCACAACGTT", "CTCGAAAGTAAGAGGA", "CTCGAAAGTGGTGTAG", "CTCGAAATCCTGCCAT", "CTCGAGGCAAGTCTGT", "CTCGAGGGTAAGTAGT", "CTCGAGGTCTGTTGAG", "CTCGGAGGTCATTAGC", "CTCGGAGGTGAAGGCT", "CTCGTACCAATGGATA", "CTCGTACTCTTTAGTC", "CTCGTCAAGAACAATC", "CTCGTCACAACTGCTA", "CTCGTCATCGGTCTAA", "CTCTAATAGTTATCGC", "CTCTGGTAGCAATCTC", "CTCTGGTAGTCCCACG", "CTCTGGTCAACACCTA", "CTCTGGTCAAGACACG", "CTCTGGTCAAGTTGTC", "CTCTGGTCAGTTCATG", "CTGAAACAGACTAGGC", "CTGAAACGTAGCGCAA", "CTGAAACGTATGGTTC", "CTGAAACTCGATAGAA", "CTGAAACTCGCCGTGA", "CTGAAACTCTGTTTGT", "CTGAAGTGTTTGGGCC", "CTGAAGTTCTGCGGCA", "CTGATCCTCAGTTGAC", "CTGCCTAGTCTCCATC", "CTGCGGACAGACTCGC", "CTGCGGACATTAGCCA", "CTGCGGATCAGCATGT", "CTGCTGTAGACTGGGT", "CTGCTGTCAAAGCAAT", "CTGGTCTAGGATTCGG", "CTGGTCTAGGTGATTA", "CTGGTCTCAGGAATGC", "CTGGTCTTCGCATGGC", "CTGTGCTCATTACCTT", "CTTAACTCAAGCGTAG", "CTTAACTTCAGCTTAG", "CTTAGGACACAGGTTT", "CTTAGGAGTCCGAATT", "CTTAGGATCAACGGGA", "CTTAGGATCACTCTTA", "CTTCTCTAGGCAGGTT", "CTTCTCTAGTCCGTAT", "CTTCTCTCAGCATACT", "CTTCTCTGTCAGAGGT", "CTTGGCTAGACAGACC", "CTTGGCTAGGACACCA", "CTTGGCTCAAAGGAAG", "CTTGGCTCAGCCACCA", "CTTGGCTCATCCCACT", "CTTGGCTGTTAGAACA", "CTTTGCGAGACCACGA", "CTTTGCGAGGAATGGA", "CTTTGCGTCCACGTGG", "GAAACTCAGAAACCTA", "GAAATGAAGCTCCTCT", "GAAATGACAACTGGCC", "GAAATGACACATGACT", "GAAATGAGTCACCCAG", "GAAATGAGTCGGATCC", "GAACATCGTAATCGTC", "GAACCTAAGTAGATGT", "GAACCTATCACTTATC", "GAACGGAAGTCAAGCG", "GAACGGACAAGGACAC", "GAAGCAGGTCGCGAAA", "GAAGCAGGTCTAGAGG", "GAAGCAGTCAAGGCTT", "GAATGAAAGAATGTGT", "GAATGAACAATCGAAA", "GAATGAACAGCCTTGG", "GAATGAATCATCGGAT", "GACACGCCAAAGGAAG", "GACCAATAGAATGTGT", "GACCAATCAGACGCCT", "GACCAATGTTATCCGA", "GACCAATGTTGGACCC", "GACCAATTCAACGGCC", "GACCTGGGTTCGTGAT", "GACGCGTCAGTCGTGC", "GACGCGTGTCGGCTCA", "GACGGCTAGGTGATAT", "GACGGCTTCAACTCTT", "GACGTGCGTCACCTAA", "GACGTGCTCCGGCACA", "GACGTTAAGACGCAAC", "GACGTTAAGACGCTTT", "GACGTTACATCTCGCT", "GACGTTAGTGTGAATA", "GACTAACGTCATCCCT", "GACTAACTCAGTCCCT", "GACTACAGTTCGTGAT", "GACTGCGAGAATCTCC", "GAGCAGAAGCGTGTCC", "GAGCAGAGTTTGCATG", "GAGCAGATCAACTCTT", "GAGGTGAGTCCGCTGA", "GAGGTGAGTGACAAAT", "GAGTCCGAGCGATGAC", "GAGTCCGAGTTAAGTG", "GAGTCCGCAATTGCTG", "GATCAGTAGGTGATAT", "GATCGATAGAAAGTGG", "GATCGATAGGATGGTC", "GATCGATGTAGCGATG", "GATCGATGTTGTTTGG", "GATCGCGCACCAGGCT", "GATCGTAAGTAGGTGC", "GATCGTAGTCCTAGCG", "GATCTAGAGCTAGCCC", "GATCTAGGTGCCTTGG", "GATGAAAAGTTGTAGA", "GATGAAACAGGCTGAA", "GATGAAACATGGTTGT", "GATGAGGAGTGGACGT", "GATGAGGTCTGGGCCA", "GATGCTAGTAGAAGGA", "GATGCTAGTGTTAAGA", "GATTCAGAGCGATGAC", "GATTCAGAGTACGTTC", "GATTCAGTCGCCAGCA", "GATTCAGTCGTCCAGG", "GCAAACTCAGACAAAT", "GCAATCACAGCTGCTG", "GCAATCATCCAACCAA", "GCACTCTCAGCGTCCA", "GCAGCCACAGCGTTCG", "GCAGTTACATTTCACT", "GCAGTTATCTTGAGAC", "GCATGATAGCCTTGAT", "GCATGATCAAGCGAGT", "GCATGATGTCACTGGC", "GCATGATGTTTAGGAA", "GCATGATTCAAACGGG", "GCATGCGAGGAACTGC", "GCATGCGCAGCTCCGA", "GCATGTAAGAATCTCC", "GCATGTAAGCGTGTCC", "GCATGTAGTTGCGCAC", "GCATGTATCGTGGACC", "GCCTCTAAGCTAGTCT", "GCCTCTAAGTCCGGTC", "GCCTCTATCGCTTAGA", "GCGACCATCACCAGGC", "GCGAGAAGTGGGTATG", "GCGCAACGTTTCGCTC", "GCGCAACTCACAACGT", "GCGCAGTGTGCTAGCC", "GCGCCAAAGCTCCTTC", "GCGCCAATCTTATCTG", "GCGCGATGTCCGAATT", "GCGGGTTAGACTTGAA", "GCGGGTTCAAGTAATG", "GCGGGTTGTTACTGAC", "GCTCCTAAGGGCATGT", "GCTCTGTGTCCATGAT", "GCTGCAGGTTACCGAT", "GCTGCGAAGAACAACT", "GCTGCGAAGCTAGCCC", "GCTGCGAAGTATTGGA", "GCTGCGATCCCGGATG", "GCTGCGATCGGCTACG", "GCTGCTTGTCTTCAAG", "GCTGGGTGTCATACTG", "GCTGGGTGTCTAGAGG", "GCTTCCAAGACATAAC", "GCTTCCAAGTTAAGTG", "GCTTGAAGTCAACTGT", "GGAAAGCCAATGTAAG", "GGAAAGCGTCTTGATG", "GGAATAAGTAAGAGAG", "GGAATAAGTTCGGGCT", "GGACAAGGTGATAAGT", "GGACAAGTCAAAGACA", "GGACAGAAGGCCGAAT", "GGACAGACAATCCAAC", "GGACAGATCAGGCGAA", "GGACAGATCCTGCAGG", "GGACAGATCCTTTCGG", "GGACATTGTCTCCCTA", "GGACGTCAGGGTGTTG", "GGACGTCCACGCATCG", "GGACGTCCATGGATGG", "GGACGTCGTCAGAAGC", "GGACGTCGTCGAGATG", "GGACGTCGTCTAGGTT", "GGACGTCGTTTAGCTG", "GGAGCAAAGCTTCGCG", "GGAGCAAGTATCACCA", "GGATGTTAGTAAGTAC", "GGATGTTTCCAGTATG", "GGCAATTCACGGCTAC", "GGCAATTCATCTCCCA", "GGCAATTGTAGAGCTG", "GGCCGATTCACTCTTA", "GGCGACTGTAAGTTCC", "GGCGTGTCACCAGGTC", "GGCGTGTCACCGATAT", "GGCGTGTTCAGCTTAG", "GGCGTGTTCGAGAGCA", "GGCTCGAAGATCACGG", "GGCTCGAAGTGACTCT", "GGCTCGACAGCTTCGG", "GGCTGGTAGTCACGCC", "GGCTGGTTCATGCATG", "GGGAATGAGCACACAG", "GGGAATGAGTGTACGG", "GGGAATGCAAAGTGCG", "GGGAATGTCACAAACC", "GGGACCTCACTGTCGG", "GGGACCTTCGAATGCT", "GGGAGATAGATGTGGC", "GGGAGATAGCGAAGGG", "GGGAGATAGTGACATA", "GGGATGAAGGGCATGT", "GGGATGAGTCTGCGGT", "GGGATGAGTTGTGGAG", "GGGCACTCATTTCAGG", "GGGCACTGTCTCCATC", "GGGCACTGTGGCAAAC", "GGGCATCCATGACATC", "GGGCATCCATTTCAGG", "GGGCATCGTGGTCTCG", "GGGTCTGCACAGGCCT", "GGGTCTGCATGAAGTA", "GGGTCTGTCATGTGGT", "GGGTCTGTCCATGAAC", "GGGTTGCCAAGCTGAG", "GGGTTGCTCGAACGGA", "GGTATTGGTACTCGCG", "GGTATTGGTCCCGACA", "GGTGTTAAGGATCGCA", "GGTGTTAGTTCCTCCA", "GTAACGTGTCACTGGC", "GTAACTGGTCACTGGC", "GTAACTGTCAGTGCAT", "GTACGTAGTCTCTTTA", "GTACTCCCACAGGTTT", "GTACTCCCACGTCTCT", "GTACTCCTCCAACCAA", "GTACTTTGTACCGTAT", "GTACTTTTCTTCGGTC", "GTAGGCCAGCTAACAA", "GTAGGCCGTTACCAGT", "GTAGTCACATCGATGT", "GTAGTCAGTCCGACGT", "GTATCTTCAGTGGGAT", "GTATCTTCATCGATGT", "GTATCTTGTACTCAAC", "GTATCTTGTCGCGGTT", "GTATCTTGTGGCCCTA", "GTATCTTTCGTGGACC", "GTATTCTCACATTAGC", "GTATTCTCACTTGGAT", "GTATTCTGTCCGTCAG", "GTATTCTTCTCTAAGG", "GTCAAGTGTGGTCCGT", "GTCACAACACGTCTCT", "GTCACGGAGCTATGCT", "GTCACGGCATCCGTGG", "GTCACGGTCTTGCCGT", "GTCATTTGTCGTCTTC", "GTCCTCACACCACGTG", "GTCCTCATCATTTGGG", "GTCCTCATCTGGAGCC", "GTCGGGTCAGGCTGAA", "GTCGTAAAGTTTAGGA", "GTCTCGTAGGCTAGAC", "GTCTCGTCATAGTAAG", "GTCTCGTTCACTTCAT", "GTCTCGTTCTGCGTAA", "GTCTTCGTCCGTTGCT", "GTCTTCGTCTACCAGA", "GTGCATAAGAACAATC", "GTGCATAAGCTCCTCT", "GTGCATAGTTCAACCA", "GTGCATATCAAGGCTT", "GTGCGGTAGTAGGCCA", "GTGCGGTCAGCGTAAG", "GTGCTTCAGAGGGATA", "GTGCTTCTCACGACTA", "GTGGGTCCATAAAGGT", "GTGGGTCCATCGATTG", "GTGGGTCGTCCAGTAT", "GTGGGTCTCCGAATGT", "GTGTGCGGTGTAAGTA", "GTGTTAGCACCATCCT", "GTGTTAGGTGAACCTT", "GTTAAGCAGGATTCGG", "GTTACAGTCCGATATG", "GTTCATTAGAAGATTC", "GTTCATTAGGCAGTCA", "GTTCATTTCCGAACGC", "GTTCTCGAGAATTCCC", "GTTCTCGCAAGAAAGG", "GTTCTCGCAGACACTT", "GTTTCTAAGAAGATTC", "GTTTCTACAGGACCCT", "TAAGAGATCTGCGACG", "TAAGTGCAGGGTTTCT", "TAAGTGCTCCAAATGC", "TACACGACAACGATCT", "TACACGACATGTAGTC", "TACACGAGTGCAACTT", "TACAGTGCAATCTACG", "TACAGTGCACAGGCCT", "TACAGTGGTAAACGCG", "TACCTTAAGTACATGA", "TACCTTATCCGATATG", "TACGGATAGAGCTGGT", "TACGGATAGGCACATG", "TACGGATAGTTTAGGA", "TACGGATGTGTTCGAT", "TACGGATTCCAAGTAC", "TACGGGCAGCCAACAG", "TACGGGCAGCGTCAAG", "TACGGGCTCTTCGGTC", "TACGGTACATGTTCCC", "TACTCATAGGTGTTAA", "TACTCATCAGATCCAT", "TACTCGCAGTAAGTAC", "TACTCGCCAGATCGGA", "TACTCGCGTCGGCATC", "TACTTACCAACTGCGC", "TACTTACCATGGGACA", "TACTTGTAGACAAAGG", "TAGACCAAGGAATCGC", "TAGAGCTGTATGAAAC", "TAGAGCTGTTGTCGCG", "TAGCCGGTCAACACAC", "TAGGCATTCCAAAGTC", "TAGTGGTCAACTGCGC", "TAGTGGTCATTCACTT", "TAGTGGTTCCTCAACC", "TAGTTGGCACGTAAGG", "TAGTTGGCAGTAACGG", "TAGTTGGGTACCGTAT", "TAGTTGGTCTTGCAAG", "TATCAGGCACCAGATT", "TATCTCACAACTGCTA", "TATCTCACACGCGAAA", "TATCTCACATTGTGCA", "TATCTCAGTTCGCTAA", "TATGCCCAGAACAATC", "TATGCCCGTCTAGCCG", "TATGCCCTCTTACCTA", "TATTACCTCGTTGCCT", "TCAACGATCAACCATG", "TCAATCTCATCCGCGA", "TCAATCTCATCTCCCA", "TCAATCTGTCAAAGAT", "TCAATCTTCGAACGGA", "TCACAAGAGTGACATA", "TCACAAGCAACGATGG", "TCACAAGCAGACTCGC", "TCACGAAGTCCGAGTC", "TCACGAATCCTATGTT", "TCAGATGCACTCGACG", "TCAGATGGTACACCGC", "TCAGCAACACCAGGCT", "TCAGCAATCGCCGTGA", "TCAGCTCAGTCGTACT", "TCAGGTAAGGCGTACA", "TCAGGTAAGTCAATAG", "TCAGGTACAGTCACTA", "TCAGGTATCTGTCCGT", "TCATTACGTCAGAAGC", "TCATTTGCATTGGCGC", "TCCACACCAGGCGATA", "TCCCGATAGTCGTTTG", "TCCCGATCAACGATGG", "TCGAGGCAGAACAATC", "TCGAGGCAGGCATGGT", "TCGCGAGAGTACGCGA", "TCGCGAGAGTCCGTAT", "TCGCGAGCACTTCTGC", "TCGGGACAGAGAACAG", "TCGGGACGTCTGCGGT", "TCGTACCCACGCATCG", "TCGTACCCATATACGC", "TCTATTGCACAGGAGT", "TCTATTGTCCTATTCA", "TCTATTGTCGTATCAG", "TCTCATAAGAATGTGT", "TCTCATACAAATTGCC", "TCTCATAGTGGACGAT", "TCTCTAAAGCTGGAAC", "TCTCTAAGTCGCATCG", "TCTCTAAGTGGCAAAC", "TCTCTAAGTTACCGAT", "TCTCTAATCCCAACGG", "TCTGAGAGTCAAACTC", "TCTGGAACACACGCTG", "TCTGGAACACCTATCC", "TCTGGAAGTCATCGGC", "TCTGGAATCGGTGTCG", "TCTTTCCGTGCAACTT", "TCTTTCCTCGTCTGCT", "TGAAAGAGTTATCACG", "TGACGGCAGGAATGGA", "TGACGGCCATATGAGA", "TGACTAGGTGTATGGG", "TGACTAGTCCACGTGG", "TGACTAGTCCTATTCA", "TGACTTTAGCCAGAAC", "TGACTTTAGCGTTGCC", "TGACTTTAGCGTTTAC", "TGAGAGGAGATCCCAT", "TGAGAGGAGCCAGGAT", "TGAGAGGAGCCGTCGT", "TGAGAGGAGGCGATAC", "TGAGAGGAGGTAAACT", "TGAGAGGCAGGAACGT", "TGAGAGGGTAAGGGCT", "TGAGCATGTTAAAGAC", "TGAGCATTCACCCGAG", "TGAGCATTCGGGAGTA", "TGAGCCGTCATGTCCC", "TGAGCCGTCCGAACGC", "TGAGCCGTCCGCTGTT", "TGAGGGAAGAGGTACC", "TGAGGGACAGACTCGC", "TGATTTCAGTACGCCC", "TGATTTCAGTGACTCT", "TGATTTCGTGAGGGTT", "TGCCAAACATGACATC", "TGCCCATCACTGTGTA", "TGCCCTAAGTCCGGTC", "TGCGCAGGTACGCACC", "TGCGCAGTCTGCCAGG", "TGCGGGTAGACGCACA", "TGCGGGTAGGGTTCCC", "TGCGGGTTCCACTCCA", "TGCGGGTTCTCAAACG", "TGCGTGGAGGTAAACT", "TGCGTGGAGGTTCCTA", "TGCGTGGAGTACACCT", "TGCGTGGGTCCCTTGT", "TGCGTGGGTTACTGAC", "TGCTACCCAGGGCATA", "TGCTACCCATAAGACA", "TGCTGCTAGGATGCGT", "TGCTGCTGTCCGTCAG", "TGGACGCAGTGTTGAA", "TGGACGCTCAGGTAAA", "TGGACGCTCTTGTTTG", "TGGCCAGAGCTACCTA", "TGGCCAGCAAGGACTG", "TGGCCAGCAATGAAAC", "TGGCCAGCACGAAAGC", "TGGCCAGGTCGGCATC", "TGGCGCATCACAACGT", "TGGCTGGGTACCCAAT", "TGGGAAGCACGTAAGG", "TGGGAAGCATGACATC", "TGGGCGTGTGTGCGTC", "TGGTTAGCAGTCGTGC", "TGGTTCCCACCGCTAG", "TGGTTCCGTCACCTAA", "TGTATTCCAATGACCT", "TGTCCCAAGTTTAGGA", "TGTCCCACATTATCTC", "TGTCCCAGTCCGTGAC", "TGTCCCATCTCTGCTG", "TGTGGTACAAGACGTG", "TGTGGTACACATCCGG", "TGTGGTAGTGCCTGCA", "TGTGGTATCCAGTAGT", "TGTGTTTAGGAATGGA", "TGTGTTTGTAGATTAG", "TGTGTTTGTATGAATG", "TTAACTCCAAAGAATC", "TTAACTCCAGGATTGG", "TTAACTCGTAATCGTC", "TTAGGCAGTTTGTTGG", "TTATGCTCACCCAGTG", "TTCCCAGAGTTACCCA", "TTCCCAGGTATTCTCT", "TTCCCAGTCATAGCAC", "TTCGAAGAGTACGCCC", "TTCGGTCAGCTAGCCC", "TTCGGTCAGGGCATGT", "TTCGGTCGTATAGTAG", "TTCGGTCTCGACCAGC", "TTCTACAAGATCGATA", "TTCTACACATAAAGGT", "TTCTACAGTACTCTCC", "TTCTACATCGCTTAGA", "TTCTACATCTGCAGTA", "TTCTCAAAGCCGCCTA", "TTCTCAACAATAGAGT", "TTCTCCTAGTCCATAC", "TTCTCCTCAATGGTCT", "TTCTTAGTCAGTGTTG", "TTGAACGAGAGCAATT", "TTGAACGAGGAGTTTA", "TTGAACGGTGAGGGAG", "TTGAACGGTGATGCCC", "TTGACTTAGACAAGCC", "TTGACTTGTTCCATGA", "TTGACTTTCACCGGGT", "TTGACTTTCAGCAACT", "TTGACTTTCCAGTAGT", "TTGCCGTCACCGAATT", "TTGCCGTTCTCTGTCG", "TTGCGTCCACCGATAT", "TTGGAACAGAAGATTC", "TTGGAACGTATATGAG", "TTGGCAAAGAGTAAGG", "TTGTAGGTCAAAGTAG", "TTTACTGCAGCATACT", "TTTACTGGTGCTAGCC", "TTTATGCAGGTTACCT", "TTTATGCGTCGAACAG", "TTTATGCTCCATTCTA", "TTTCCTCCAGGATCGA", "TTTCCTCGTGGCGAAT", "TTTGCGCAGACAGACC", "TTTGGTTAGACAGGCT", "TTTGGTTCACCAGATT", "TTTGGTTCACGAAGCA", "TTTGGTTTCCTTTCGG", "TTTGTCAAGAATGTGT", "TTTGTCATCGAATGCT", "TTTGTCATCTGTTTGT" ), c("StandardpcaUMAP2D_1", "StandardpcaUMAP2D_2"))), subscript = NA_integer_, index = 10), class = c("subscriptOutOfBoundsError", "error", "condition"))): error in evaluating the argument 'data' in selecting a method for function 'slingshot': subscript out of bounds
CellDimPlot(
pancreas_sub,
group.by = "SubCellType",
reduction = "UMAP",
lineages = paste0("Lineage", 1:2),
lineages_span = 0.1
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
# 3D lineage
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2025-09-20 13:58:43] Start standard scop workflow...
#> ℹ [2025-09-20 13:58:43] Checking a list of <Seurat> object...
#> ℹ [2025-09-20 13:58:43] Data 1/1 of the `srt_list` has been log-normalized
#> ℹ [2025-09-20 13:58:43] Perform `Seurat::FindVariableFeatures()` on the data 1/1 of the `srt_list`...
#> ℹ [2025-09-20 13:58:44] Use the separate HVF from srt_list
#> ℹ [2025-09-20 13:58:44] Number of available HVF: 2000
#> ℹ [2025-09-20 13:58:44] Finished check
#> ℹ [2025-09-20 13:58:44] Perform `Seurat::ScaleData()`
#> ℹ [2025-09-20 13:58:45] Perform pca linear dimension reduction
#> StandardPC_ 1
#> Positive: Aplp1, Cpe, Gnas, Fam183b, Map1b, Hmgn3, Pcsk1n, Chga, Tuba1a, Bex2
#> Syt13, Isl1, 1700086L19Rik, Pax6, Chgb, Scgn, Rbp4, Scg3, Gch1, Camk2n1
#> Cryba2, Pcsk2, Pyy, Tspan7, Mafb, Hist3h2ba, Dbpht2, Abcc8, Rap1b, Slc38a5
#> Negative: Spp1, Anxa2, Sparc, Dbi, 1700011H14Rik, Wfdc2, Gsta3, Adamts1, Clu, Mgst1
#> Bicc1, Ldha, Vim, Cldn3, Cyr61, Rps2, Mt1, Ptn, Phgdh, Nudt19
#> Smtnl2, Smco4, Habp2, Mt2, Col18a1, Rpl12, Galk1, Cldn10, Acot1, Ccnd1
#> StandardPC_ 2
#> Positive: Rbp4, Tagln2, Tuba1b, Fkbp2, Pyy, Pcsk2, Iapp, Tmem27, Meis2, Tubb4b
#> Pcsk1n, Dbpht2, Rap1b, Dynll1, Tubb2a, Sdf2l1, Scgn, 1700086L19Rik, Scg2, Abcc8
#> Atp1b1, Hspa5, Fam183b, Papss2, Slc38a5, Scg3, Mageh1, Tspan7, Ppp1r1a, Ociad2
#> Negative: Neurog3, Btbd17, Gadd45a, Ppp1r14a, Neurod2, Sox4, Smarcd2, Mdk, Pax4, Btg2
#> Sult2b1, Hes6, Grasp, Igfbpl1, Gpx2, Cbfa2t3, Foxa3, Shf, Mfng, Tmsb4x
#> Amotl2, Gdpd1, Cdc14b, Epb42, Rcor2, Cotl1, Upk3bl, Rbfox3, Cldn6, Cer1
#> StandardPC_ 3
#> Positive: Nusap1, Top2a, Birc5, Aurkb, Cdca8, Pbk, Mki67, Tpx2, Plk1, Ccnb1
#> 2810417H13Rik, Incenp, Cenpf, Ccna2, Prc1, Racgap1, Cdk1, Aurka, Cdca3, Hmmr
#> Spc24, Kif23, Sgol1, Cenpe, Cdc20, Hist1h1b, Cdca2, Mxd3, Kif22, Ska1
#> Negative: Anxa5, Pdzk1ip1, Acot1, Tpm1, Anxa2, Dcdc2a, Capg, Sparc, Ttr, Pamr1
#> Clu, Cxcl12, Ndrg2, Hnf1aos1, Gas6, Gsta3, Krt18, Ces1d, Atp1b1, Muc1
#> Hhex, Acadm, Spp1, Enpp2, Bcl2l14, Sat1, Smtnl2, 1700011H14Rik, Tgm2, Fam159a
#> StandardPC_ 4
#> Positive: Glud1, Tm4sf4, Akr1c19, Cldn4, Runx1t1, Fev, Pou3f4, Gm43861, Pgrmc1, Arx
#> Cd200, Lrpprc, Hmgn3, Ppp1r14c, Pam, Etv1, Tsc22d1, Slc25a5, Akap17b, Pgf
#> Fam43a, Emb, Jun, Krt8, Dnajc12, Mid1ip1, Ids, Rgs17, Uchl1, Alcam
#> Negative: Ins2, Ins1, Ppp1r1a, Nnat, Calr, Sytl4, Sdf2l1, Iapp, Pdia6, Mapt
#> G6pc2, C2cd4b, Npy, Gng12, P2ry1, Ero1lb, Adra2a, Papss2, Arhgap36, Fam151a
#> Dlk1, Creld2, Gip, Tmem215, Gm27033, Cntfr, Prss53, C2cd4a, Lyve1, Ociad2
#> StandardPC_ 5
#> Positive: Pdx1, Nkx6-1, Npepl1, Cldn4, Cryba2, Fev, Jun, Chgb, Gng12, Adra2a
#> Mnx1, Sytl4, Pdk3, Gm27033, Nnat, Chga, Ins2, 1110012L19Rik, Enho, Krt7
#> Mlxipl, Tmsb10, Flrt1, Pax4, Tubb3, Prrg2, Gars, Frzb, BC023829, Gm2694
#> Negative: Irx2, Irx1, Gcg, Ctxn2, Tmem27, Ctsz, Tmsb15l, Nap1l5, Pou6f2, Gria2
#> Ghrl, Peg10, Smarca1, Arx, Lrpap1, Rgs4, Ttr, Gast, Tmsb15b2, Serpina1b
#> Slc16a10, Wnk3, Ly6e, Auts2, Sct, Arg1, Dusp10, Sphkap, Dock11, Edn3
#> ℹ [2025-09-20 13:58:45] Perform `Seurat::FindClusters()` with louvain and `cluster_resolution` = 0.6
#> ℹ [2025-09-20 13:58:46] Reorder clusters...
#> ! [2025-09-20 13:58:46] Using `Seurat::AggregateExpression()` to calculate pseudo-bulk data for <Assay5>
#> ℹ [2025-09-20 13:58:46] Perform umap nonlinear dimension reduction
#> ℹ [2025-09-20 13:58:46] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-09-20 13:58:46] UMAP will return its model
#> Warning: Key ‘StandardpcaUMAP2D_’ taken, using ‘standardpcaumap2d_’ instead
#> ℹ [2025-09-20 13:58:50] Non-linear dimensionality reduction (umap) using (Standardpca) dims (1-50) as input
#> ℹ [2025-09-20 13:58:50] UMAP will return its model
#> Warning: Key ‘StandardpcaUMAP3D_’ taken, using ‘standardpcaumap3d_’ instead
#> ✔ [2025-09-20 13:58:55] Run scop standard workflow done
pancreas_sub <- RunSlingshot(
pancreas_sub,
group.by = "SubCellType",
reduction = "StandardpcaUMAP3D"
)
CellDimPlot(
pancreas_sub,
group.by = "SubCellType",
reduction = "UMAP",
lineages = paste0("Lineage", 1:2),
lineages_span = 0.1,
lineages_trim = c(0.05, 0.95)
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
