stemangiola/tidybulk

Issues

• limma:MakeContrasts integration issues

  #309 opened 4 months ago by aodainic7
  2

• Add the method to simplify complete confounders is they are not factor of interest

  #301 opened 7 months ago by stemangiola
  0

• Improve the documentation for `tidybulk`

  #282 opened a year ago by stemangiola
  29

• Prepare for upcoming Seurat v5 release

  #298 opened 8 months ago by Gesmira
  0

• the attribute "internals" $ tt_columns abundance_scaled, carries the environment with it inflating the RDS file size

  #295 opened 9 months ago by stemangiola
  0

• in `test_gene_rank` check if any feature is NA, because pivot_feature will fail

  #292 opened 9 months ago by stemangiola
  0

• for SE save internals within the metadata rather than attributes.

  #240 opened 2 years ago by stemangiola
  0

• Feedback from talk: get_bibliography

  #180 opened 3 years ago by stemangiola
  1

• `tidybulk` Replace pivot_* with select_columns_*

  #181 opened 3 years ago by stemangiola
  3

• `tidybulk` Remove hard dependency for `DESeq2`

  #286 opened 9 months ago by stemangiola
  12

• turn pseudobulk from scRNAseq with logCPM value back to a seurat object with counts value?

  #285 opened 10 months ago by jiangzh-coder
  2

• test

  #280 opened a year ago by stemangiola
  0

• Warning in CHECK, mistery

  #273 opened a year ago by stemangiola
  0

• Remove batch effect in test_differential_abundance

  #270 opened a year ago by jianwu1
  0

• Allow logFC shrinkage in DESeq

  #224 opened 3 years ago by antass
  4

• Use feature instead of transcript

  #182 opened a year ago by stemangiola
  1

• "Proportion of variance explained" values on reduce_dimensions() output

  #253 opened a year ago by canholyavkin
  1

• Design and contrasts for tidybulk test differential abundance function

  #264 opened a year ago by adityamahadevaniyer
  9

• pathway analysis using tidybulk

  #263 opened a year ago by adityamahadevaniyer
  8

• github actions give preflight error for the whole tidy stack

  #259 opened 2 years ago by stemangiola
  1

• ERROR; return code from pthread_create() is 22

  #261 opened 2 years ago by indapa
  3

• DEG Analysis Between Single Group with Multiple Groups

  #245 opened 2 years ago by canholyavkin
  6

• github action mac fail

  #243 opened 2 years ago by stemangiola
  1

• Retain count_scaled in as_SummarizedExperiment()

  #212 opened 2 years ago by jianwu1
  3

• pass ... ellipse argument to test_differential_abundance

  #136 opened 2 years ago by stemangiola
  4

• import from tximeta RangedSummarizedExperiment ?

  #184 opened 2 years ago by AMChalkie
  23

• pivot_sample and pivot_transcript convert .sample and .feature to sample and feature

  #222 opened 2 years ago by mblue9
  2

• create_tt_from_bam_sam_bulk function recuires org.Hs database and is therefore incompatible with other organisms

  #221 opened 2 years ago by richardstoeckl
  2

• Using contrasts instead of .contrasts is silently ignored

  #208 opened 2 years ago by mblue9
  2

• Issue with DESeq2

  #215 opened 2 years ago by shaman-narayanasamy
  9

• Normalization method (scaling)

  #225 opened 3 years ago by ConYel
  9

• Use data.table in aggregate_duplicate() for huge data frames

  #186 opened 3 years ago by RAGG3D
  3

• Arguement "minimum_proportion" of the function "keep_abundant()" appears to not do anything

  #192 opened 3 years ago by JohnHadish
  2

• Confused on TidyBulk's desired format

  #187 opened 3 years ago by JohnHadish
  2

• Fixing the github actions

  #189 opened 3 years ago by stemangiola
  1

• test_gene_enrichment with tidySummarizedExperiment input

  #174 opened 3 years ago by mblue9
  10

• Fixing github action

  #168 opened 3 years ago by stemangiola
  2

• test_gene_enrichment error: object '.transcript' not found

  #166 opened 3 years ago by mblue9
  1

• Consistent column names for differential expression results

  #120 opened 3 years ago by AMChalkie
  10

• limma_voom sample weighing in test_differential_abundance?

  #117 opened 3 years ago by AMChalkie
  8

• curate bibliography list

  #121 opened 3 years ago by stemangiola
  0

• ERROR; return code from pthread_create() is 22

  #145 opened 3 years ago by stemangiola
  1

• MacOS build issues

  #144 opened 3 years ago by stemangiola
  1

• Survival Analysis

  #155 opened 3 years ago by france-hub
  2

• double check DESeq2

  #113 opened 4 years ago by stemangiola
  16

• Quiet parameter for keep_variable()

  #133 opened 4 years ago by canholyavkin
  8

• directionality of log2FoldChange (DESeq2) opposite to voom and edgeR

  #123 opened 4 years ago by AMChalkie
  11

• fucntion => function in method descriptions

  #118 opened 4 years ago by AMChalkie
  1

• for scaling check the presence of a multiplier column

  #122 opened 4 years ago by stemangiola
  1

• Dropping parameters significant_threshold and fill_missing_values

  #109 opened 4 years ago by stemangiola
  2