Hello,
I started using FastReseg since Nov 2025. There seems to be a recent update on FastReseg and I switched to the latest version on December 2025 and since then, updated_perCellExprs slot in the fastReseg_full_pipeline's ouput object only contains small fractions of entire updated cells.
I ran the same script with the same data before an update and I did not have an issue.
Part of the output object looks like this:
$ updated_perCellDT :Classes ‘data.table’ and 'data.frame': 65281 obs. of 6 variables:
..$ updated_cellID : chr [1:65281] "c_1_1_1" "c_1_1_10" "c_1_1_100" "c_1_1_101" ...
..$ updated_celltype: chr [1:65281] "Stem" "Enterocytes" "Cycling B" "Enterocytes" ...
..$ x : num [1:65281] 17425 17415 17532 17614 17594 ...
..$ y : num [1:65281] 8411 8360 8210 8205 8209 ...
..$ z : num [1:65281] 2.62 4.28 3.35 2.94 3.63 ...
..$ reSeg_action : chr [1:65281] "none" "none" "none" "none" ...
..- attr(*, ".internal.selfref")=
$ updated_perCellExprs:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. ..@ i : int [1:518201] 1 5 10 11 18 38 51 60 64 66 ...
.. ..@ p : int [1:710] 0 864 1079 1969 3996 4217 4565 5269 6426 6986 ...
.. ..@ Dim : int [1:2] 6175 709
.. ..@ Dimnames:List of 2
.. .. ..$ : chr [1:6175] "A1BG" "A2M" "AAAS" "AAK1" ...
.. .. ..$ : chr [1:709] "c_1_1_1" "c_1_1_10" "c_1_1_100" "c_1_1_101" ...
.. ..@ x : num [1:518201] 1 1 1 1 2 1 1 1 1 1 ...
.. ..@ factors : list()
We have around 65k cells but the updated_perCellExprs now only has 709 cells.
Could you help us with this?
We have this same issue for multiple datasets.
best,
Koichi
Hello,
I started using FastReseg since Nov 2025. There seems to be a recent update on FastReseg and I switched to the latest version on December 2025 and since then, updated_perCellExprs slot in the fastReseg_full_pipeline's ouput object only contains small fractions of entire updated cells.
I ran the same script with the same data before an update and I did not have an issue.
Part of the output object looks like this:
$ updated_perCellDT :Classes ‘data.table’ and 'data.frame': 65281 obs. of 6 variables:
..$ updated_cellID : chr [1:65281] "c_1_1_1" "c_1_1_10" "c_1_1_100" "c_1_1_101" ...
..$ updated_celltype: chr [1:65281] "Stem" "Enterocytes" "Cycling B" "Enterocytes" ...
..$ x : num [1:65281] 17425 17415 17532 17614 17594 ...
..$ y : num [1:65281] 8411 8360 8210 8205 8209 ...
..$ z : num [1:65281] 2.62 4.28 3.35 2.94 3.63 ...
..$ reSeg_action : chr [1:65281] "none" "none" "none" "none" ...
..- attr(*, ".internal.selfref")=
$ updated_perCellExprs:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. ..@ i : int [1:518201] 1 5 10 11 18 38 51 60 64 66 ...
.. ..@ p : int [1:710] 0 864 1079 1969 3996 4217 4565 5269 6426 6986 ...
.. ..@ Dim : int [1:2] 6175 709
.. ..@ Dimnames:List of 2
.. .. ..$ : chr [1:6175] "A1BG" "A2M" "AAAS" "AAK1" ...
.. .. ..$ : chr [1:709] "c_1_1_1" "c_1_1_10" "c_1_1_100" "c_1_1_101" ...
.. ..@ x : num [1:518201] 1 1 1 1 2 1 1 1 1 1 ...
.. ..@ factors : list()
We have around 65k cells but the updated_perCellExprs now only has 709 cells.
Could you help us with this?
We have this same issue for multiple datasets.
best,
Koichi