dmcable/spacexr

Issues

• Encountered infinite loop while running run.RCTD()

  #226 opened 2 months ago by gaohaohoa
  0

• please,i have loading this package,but it still give me this erro

  #194 opened a year ago by seekning
  5

• Strategy needed: RCTD deconvolution for large-scale mouse liver spatial transcriptomics data (99,894 spots)

  #225 opened 4 months ago by Lao-Tz
  0

• when i run" GSM6506110_RCTD <- run.RCTD(GSM6506110, doublet_mode = 'doublet')"

  #224 opened 4 months ago by seekning
  0

• Creating a combined reference from multiple datasets

  #202 opened a year ago by OdmaaBayar
  3

• Question about spot filtering in create.RCTD step

  #223 opened 4 months ago by Yijia-Jiang
  0

• Driver genes

  #222 opened 5 months ago by p-gueguen
  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 opened 5 months ago by Roger-GOAT
  1

• 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 opened 5 months ago by reinertanalytics
  0

• Error no cell types passed weight threshold on full mode

  #220 opened 5 months ago by Yijia-Jiang
  0

• Question on deconvolution using RCTD

  #219 opened 5 months ago by wzdrgi
  0

• Question about CSIDE

  #217 opened 5 months ago by nilchia
  0

• Unable to run deconvolution after data spliting

  #216 opened 5 months ago by Yijia-Jiang
  0

• Behavior of RCTD multi-cores

  #215 opened 6 months ago by WuRAFY
  0

• Interactive selection of cells in spatial data for covariate assignment?

  #214 opened 6 months ago by alexwskh
  0

• Running CSIDE on across multiple tissue sections

  #213 opened 6 months ago by suerle
  0

• RCTD results--many NA values

  #212 opened 6 months ago by liyiwang0725
  2

• Incorporate Spotclean results with RCTD

  #199 opened a year ago by ayusyarif
  1

• 0 overlapping genes between query and reference error

  #211 opened 7 months ago by billyt-gene
  0

• Issue with class_df in create.RCTD

  #210 opened 8 months ago by Jiayi-Zheng
  0

• Missing files meta_data.csv and dge.csv

  #209 opened 8 months ago by ChangCharity
  0

• NA in RCTD result

  #208 opened 9 months ago by yrsong001
  0

• Merge RCTD object

  #207 opened 9 months ago by sang-15
  0

• RCTD results

  #205 opened 10 months ago by balthasar0810
  0

• Error message on run.RCTD "could not find function "solveIRWLS.weights"

  #181 opened a year ago by lyndsey13sk
  3

• Question about puck@counts matrix

  #204 opened 10 months ago by Mollyx06
  1

• A question about "RCTD <- run.RCTD(RCTD, doublet_mode = "doublet")"

  #203 opened 10 months ago by M-jk22
  0

• RCTD on multiple spatially resolved transcriptomic datasets? Is it possible?

  #201 opened a year ago by MatteoRiva95
  0

• Meta regression steps and Error

  #191 opened a year ago by meaksu
  1

• could not find function "solveIRWLS.weights

  #200 opened a year ago by MingyuYang-Yale
  1

• enhancement for RCTD function gather_results to increase speed.

  #196 opened a year ago by szimmerman92
  1

• Advice on choosing UMI_min_sigma for probe-based methods

  #197 opened a year ago by dpcook
  0

• RCTD method's cell type weights doesn't sum to 1

  #193 opened a year ago by Lahiru-lsb
  1

• Population meta analysis multi-covariate error

  #195 opened a year ago by zweiss22
  0

• Error when running run.CSIDE.replicates, doublet_mode not found in myRCTD@config

  #177 opened 2 years ago by rpisalive
  5

• How are the spots assigned to doublet_certain vs. doublet_uncertain and reject?

  #190 opened a year ago by dbuszta
  0

• p vs p_cross with disease replicates?

  #189 opened a year ago by zweiss22
  0

• Reference data for J20 Hippocampus Slide-seq analysis

  #188 opened a year ago by Vivianstats
  1

• running C-SIDE to find DE for one cell type between different tissues

  #187 opened a year ago by LooLipin
  1

• some parameters are set to the CSIDE vignette values, which are intended for testing but not proper execution.

  #179 opened a year ago by sopenaml
  6

• medv hardcoded value in run.CSIDE.single

  #183 opened a year ago by baptiste-grs
  2

• `gather_results` is no longer exported

  #184 opened a year ago by ppm1337
  1

• CSIDE results csv files all vs. sig

  #185 opened a year ago by meaksu
  1

• Error while making reference files

  #186 opened a year ago by BaluPai
  1

• Is it possible to get simulation matrix like singcell dada?

  #180 opened a year ago by lilwo
  2

• Put RCTD on Bioconductor

  #178 opened a year ago by estellad
  1

• Differential Expression with Multiple Experimental Replicates and Multiple Regions

  #176 opened 2 years ago by rpisalive
  2

• C-SIDE without RCTD cell type estimates

  #174 opened 2 years ago by KaBach
  1

• Slide-seq spatial counts data

  #175 opened 2 years ago by strawberry098
  0

• Clustering using RCTD output

  #173 opened 2 years ago by oghzzang
  0