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Issues list

limma:MakeContrasts integration issues bug Something isn't working
#309 by aodainic7 was closed Feb 7, 2024
1
@stemangiola
2
in test_gene_rank check if any feature is NA, because pivot_feature will fail
#292 by stemangiola was closed Sep 8, 2023
tidybulk Remove hard dependency for DESeq2
#286 by stemangiola was closed Aug 29, 2023
1
12
turn pseudobulk from scRNAseq with logCPM value back to a seurat object with counts value?
#285 by jiangzh-coder was closed Jul 26, 2023
2
test
#280 by stemangiola was closed Jul 19, 2023
Remove batch effect in test_differential_abundance
#270 by jianwu1 was closed May 29, 2023
Design and contrasts for tidybulk test differential abundance function
#264 by adityamahadevaniyer was closed Mar 5, 2023
9
ERROR; return code from pthread_create() is 22
#261 by indapa was closed Nov 14, 2022
3
github actions give preflight error for the whole tidy stack
#259 by stemangiola was closed Nov 14, 2022
1
1
"Proportion of variance explained" values on reduce_dimensions() output
#253 by canholyavkin was closed Mar 5, 2023
1
1
DEG Analysis Between Single Group with Multiple Groups
#245 by canholyavkin was closed Jun 28, 2022
6
github action mac fail
#243 by stemangiola was closed Jun 26, 2022
1
Normalization method (scaling) enhancement New feature or request
#225 by ConYel was closed Nov 6, 2021
1
9
pivot_sample and pivot_transcript convert .sample and .feature to sample and feature
#222 by mblue9 was closed Jun 26, 2022
1
2
create_tt_from_bam_sam_bulk function recuires org.Hs database and is therefore incompatible with other organisms enhancement New feature or request
#221 by richardstoeckl was closed Jun 26, 2022
1
2
Issue with DESeq2 bug Something isn't working
#215 by shaman-narayanasamy was closed Jun 24, 2022
9
Retain count_scaled in as_SummarizedExperiment()
#212 by jianwu1 was closed Jun 24, 2022
3
Using contrasts instead of .contrasts is silently ignored
#208 by mblue9 was closed Jun 26, 2022
1
2
Arguement "minimum_proportion" of the function "keep_abundant()" appears to not do anything
#192 by JohnHadish was closed Jun 23, 2021
2
Fixing the github actions
#189 by stemangiola was closed Jun 4, 2021
2
1
Confused on TidyBulk's desired format
#187 by JohnHadish was closed Jun 5, 2021
1
2
Use data.table in aggregate_duplicate() for huge data frames
#186 by RAGG3D was closed Jul 12, 2021
1
3
import from tximeta RangedSummarizedExperiment ?
#184 by AMChalkie was closed Jun 26, 2022
2
23
Use feature instead of transcript enhancement New feature or request
#182 by stemangiola was closed Mar 5, 2023
1
test_gene_enrichment with tidySummarizedExperiment input
#174 by mblue9 was closed Apr 29, 2021
1
10
ProTip! Updated in the last three days: updated:>2025-03-05.