dmcable spacexr issues - Githubissues

dmcable / spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

GNU General Public License v3.0

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Question about spot filtering in create.RCTD step

#223 Yijia-Jiang opened 1 day ago
0
Driver genes

#222 p-gueguen opened 1 week ago
0
Error in `[<-.data.frame`(`*tmp*`, col, value = c("KC33_AAACCCAAGTAGTCAA", : replacement has 76211 rows, data has 694321 Calls: read_reference -> read_adata -> read_df -> [<- -> [<-.data.frame

#221 reinertanalytics opened 2 weeks ago
0
Error no cell types passed weight threshold on full mode

#220 Yijia-Jiang opened 3 weeks ago
0
Question on deconvolution using RCTD

#219 wzdrgi opened 3 weeks ago
0
"Cannot assign an object of class 'numeric' to the slot @‘counts’ in an object of class 'SpatialRNA'; is(value, 'dgCMatrix') is not TRUE."

#218 Roger-GOAT opened 4 weeks ago
1
Question about CSIDE

#217 nilchia opened 1 month ago
0
Unable to run deconvolution after data spliting

#216 Yijia-Jiang opened 1 month ago
0
Behavior of RCTD multi-cores

#215 WuRAFY opened 1 month ago
0
Interactive selection of cells in spatial data for covariate assignment?

#214 alexwskh opened 1 month ago
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Running CSIDE on across multiple tissue sections

#213 suerle opened 1 month ago
0
RCTD results--many NA values

#212 liyiwang0725 closed 1 month ago
2
0 overlapping genes between query and reference error

#211 billyt-gene opened 2 months ago
0
Issue with class_df in create.RCTD

#210 Jiayi-Zheng opened 3 months ago
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Missing files meta_data.csv and dge.csv

#209 ChangCharity opened 3 months ago
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NA in RCTD result

#208 yrsong001 opened 4 months ago
0
Merge RCTD object

#207 sang-15 opened 4 months ago
0
Speed improvements

#206 jpromeror opened 5 months ago
0
RCTD results

#205 balthasar0810 opened 5 months ago
0
Question about puck@counts matrix

#204 Mollyx06 closed 6 months ago
1
A question about "RCTD <- run.RCTD(RCTD, doublet_mode = "doublet")"

#203 M-jk22 opened 6 months ago
0
Creating a combined reference from multiple datasets

#202 OdmaaBayar opened 6 months ago
2
RCTD on multiple spatially resolved transcriptomic datasets? Is it possible?

#201 MatteoRiva95 opened 6 months ago
0
could not find function "solveIRWLS.weights

#200 MingyuYang-Yale closed 7 months ago
1
Incorporate Spotclean results with RCTD

#199 ayusyarif opened 7 months ago
1
Fixed bug in meta.design.matrix

#198 letaylor opened 7 months ago
0
Advice on choosing UMI_min_sigma for probe-based methods

#197 dpcook opened 8 months ago
0
enhancement for RCTD function gather_results to increase speed.

#196 szimmerman92 opened 8 months ago
1
Population meta analysis multi-covariate error

#195 zweiss22 opened 8 months ago
0
please,i have loading this package,but it still give me this erro

#194 seekning opened 9 months ago
3
RCTD method's cell type weights doesn't sum to 1

#193 Lahiru-lsb opened 9 months ago
1
Update README.md

#192 Anacristina0914 closed 8 months ago
0
Meta regression steps and Error

#191 meaksu opened 9 months ago
1
How are the spots assigned to doublet_certain vs. doublet_uncertain and reject?

#190 dbuszta opened 10 months ago
0
p vs p_cross with disease replicates?

#189 zweiss22 opened 10 months ago
0
Reference data for J20 Hippocampus Slide-seq analysis

#188 Vivianstats opened 10 months ago
1
running C-SIDE to find DE for one cell type between different tissues

#187 LooLipin closed 10 months ago
1
Error while making reference files

#186 BaluPai closed 10 months ago
1
CSIDE results csv files all vs. sig

#185 meaksu opened 11 months ago
1
`gather_results` is no longer exported

#184 ppm1337 opened 11 months ago
1
medv hardcoded value in run.CSIDE.single

#183 baptiste-grs closed 10 months ago
2
updated manual, added warning, and added source for vignette 4

#182 dmcable closed 1 year ago
0
Error message on run.RCTD "could not find function "solveIRWLS.weights"

#181 lyndsey13sk closed 11 months ago
3
Is it possible to get simulation matrix like singcell dada?

#180 lilwo closed 11 months ago
2
some parameters are set to the CSIDE vignette values, which are intended for testing but not proper execution.

#179 sopenaml opened 1 year ago
6
Put RCTD on Bioconductor

#178 estellad closed 1 year ago
1
Error when running run.CSIDE.replicates, doublet_mode not found in myRCTD@config

#177 rpisalive opened 1 year ago
5
Differential Expression with Multiple Experimental Replicates and Multiple Regions

#176 rpisalive closed 1 year ago
2
Slide-seq spatial counts data

#175 strawberry098 closed 1 year ago
0
C-SIDE without RCTD cell type estimates

#174 KaBach opened 1 year ago
1