From 17889744ada295fe9ca6b624f8dee83955d1abc1 Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Tue, 2 Apr 2024 16:41:29 -0400 Subject: [PATCH] tidy --- metadata/counts_multimap_sample_sheet.csv | 7 - ...ounts_multimap_sample_sheet_fulllength.csv | 7 - metadata/counts_sample_sheet.csv | 7 - metadata/counts_sample_sheet_fulllength.csv | 7 - metadata/counts_sample_sheet_gencode.csv | 7 - metadata/counts_sample_sheet_pbmc.csv | 4 - metadata/counts_sample_sheet_pbmc_cr.csv | 4 - metadata/counts_sample_sheet_unfiltered.csv | 7 - numbers/dge-dtu-451lu.Rmd | 93 -- numbers/dge-dtu-451lu.html | 923 --------------- numbers/novel-isoforms.Rmd | 90 -- numbers/novel-isoforms.html | 1004 ----------------- 12 files changed, 2160 deletions(-) delete mode 100644 metadata/counts_multimap_sample_sheet.csv delete mode 100644 metadata/counts_multimap_sample_sheet_fulllength.csv delete mode 100644 metadata/counts_sample_sheet.csv delete mode 100644 metadata/counts_sample_sheet_fulllength.csv delete mode 100644 metadata/counts_sample_sheet_gencode.csv delete mode 100644 metadata/counts_sample_sheet_pbmc.csv delete mode 100644 metadata/counts_sample_sheet_pbmc_cr.csv delete mode 100644 metadata/counts_sample_sheet_unfiltered.csv delete mode 100644 numbers/dge-dtu-451lu.Rmd delete mode 100644 numbers/dge-dtu-451lu.html delete mode 100644 numbers/novel-isoforms.Rmd delete mode 100644 numbers/novel-isoforms.html diff --git a/metadata/counts_multimap_sample_sheet.csv b/metadata/counts_multimap_sample_sheet.csv deleted file mode 100644 index cd26611..0000000 --- a/metadata/counts_multimap_sample_sheet.csv +++ /dev/null @@ -1,7 +0,0 @@ -sample_id,tissue,version,file_scutrquant,file_cellranger,file_multimap -heart_1k_v2_fastq,heart,v2,data/sce/utrome_mm10_v1/heart_1k_v2_fastq.genes.Rds,data/counts/heart_1k_v2_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1/heart_1k_v2_fastq/gene_multimapping.tsv.gz -heart_1k_v3_fastq,heart,v3,data/sce/utrome_mm10_v1/heart_1k_v3_fastq.genes.Rds,data/counts/heart_1k_v3_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1/heart_1k_v3_fastq/gene_multimapping.tsv.gz -heart_10k_v3_fastq,heart,v3,data/sce/utrome_mm10_v1/heart_10k_v3_fastq.genes.Rds,data/counts/heart_10k_v3_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1/heart_10k_v3_fastq/gene_multimapping.tsv.gz -neuron_1k_v2_fastq,neuron,v2,data/sce/utrome_mm10_v1/neuron_1k_v2_fastq.genes.Rds,data/counts/neuron_1k_v2_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1/neuron_1k_v2_fastq/gene_multimapping.tsv.gz -neuron_1k_v3_fastq,neuron,v3,data/sce/utrome_mm10_v1/neuron_1k_v3_fastq.genes.Rds,data/counts/neuron_1k_v3_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1/neuron_1k_v3_fastq/gene_multimapping.tsv.gz -neuron_10k_v3_fastq,neuron,v3,data/sce/utrome_mm10_v1/neuron_10k_v3_fastq.genes.Rds,data/counts/neuron_10k_v3_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1/neuron_10k_v3_fastq/gene_multimapping.tsv.gz diff --git a/metadata/counts_multimap_sample_sheet_fulllength.csv b/metadata/counts_multimap_sample_sheet_fulllength.csv deleted file mode 100644 index b6a85db..0000000 --- a/metadata/counts_multimap_sample_sheet_fulllength.csv +++ /dev/null @@ -1,7 +0,0 @@ -sample_id,tissue,version,file_scutrquant,file_cellranger,file_multimap -heart_1k_v2_fastq,heart,v2,data/sce/utrome_mm10_v1_fulllength/heart_1k_v2_fastq.genes.Rds,data/counts/heart_1k_v2_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1_fulllength/heart_1k_v2_fastq/gene_multimapping.tsv.gz -heart_1k_v3_fastq,heart,v3,data/sce/utrome_mm10_v1_fulllength/heart_1k_v3_fastq.genes.Rds,data/counts/heart_1k_v3_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1_fulllength/heart_1k_v3_fastq/gene_multimapping.tsv.gz -heart_10k_v3_fastq,heart,v3,data/sce/utrome_mm10_v1_fulllength/heart_10k_v3_fastq.genes.Rds,data/counts/heart_10k_v3_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1_fulllength/heart_10k_v3_fastq/gene_multimapping.tsv.gz -neuron_1k_v2_fastq,neuron,v2,data/sce/utrome_mm10_v1_fulllength/neuron_1k_v2_fastq.genes.Rds,data/counts/neuron_1k_v2_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1_fulllength/neuron_1k_v2_fastq/gene_multimapping.tsv.gz -neuron_1k_v3_fastq,neuron,v3,data/sce/utrome_mm10_v1_fulllength/neuron_1k_v3_fastq.genes.Rds,data/counts/neuron_1k_v3_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1_fulllength/neuron_1k_v3_fastq/gene_multimapping.tsv.gz -neuron_10k_v3_fastq,neuron,v3,data/sce/utrome_mm10_v1_fulllength/neuron_10k_v3_fastq.genes.Rds,data/counts/neuron_10k_v3_filtered_feature_bc_matrix.h5,data/kallisto/multimapping/utrome_mm10_v1_fulllength/neuron_10k_v3_fastq/gene_multimapping.tsv.gz diff --git a/metadata/counts_sample_sheet.csv b/metadata/counts_sample_sheet.csv deleted file mode 100644 index be90420..0000000 --- a/metadata/counts_sample_sheet.csv +++ /dev/null @@ -1,7 +0,0 @@ -sample_id,tissue,version,file_scutrquant,file_cellranger -heart_1k_v2_fastq,heart,v2,data/sce/heart_1k_v2_fastq.utrome.txs.Rds,data/counts/heart_1k_v2_filtered_feature_bc_matrix.h5 -heart_1k_v3_fastq,heart,v3,data/sce/heart_1k_v3_fastq.utrome.txs.Rds,data/counts/heart_1k_v3_filtered_feature_bc_matrix.h5 -heart_10k_v3_fastq,heart,v3,data/sce/heart_10k_v3_fastq.utrome.txs.Rds,data/counts/heart_10k_v3_filtered_feature_bc_matrix.h5 -neuron_1k_v2_fastq,neuron,v2,data/sce/neuron_1k_v2_fastq.utrome.txs.Rds,data/counts/neuron_1k_v2_filtered_feature_bc_matrix.h5 -neuron_1k_v3_fastq,neuron,v3,data/sce/neuron_1k_v3_fastq.utrome.txs.Rds,data/counts/neuron_1k_v3_filtered_feature_bc_matrix.h5 -neuron_10k_v3_fastq,neuron,v3,data/sce/neuron_10k_v3_fastq.utrome.txs.Rds,data/counts/neuron_10k_v3_filtered_feature_bc_matrix.h5 diff --git a/metadata/counts_sample_sheet_fulllength.csv b/metadata/counts_sample_sheet_fulllength.csv deleted file mode 100644 index dd96ca0..0000000 --- a/metadata/counts_sample_sheet_fulllength.csv +++ /dev/null @@ -1,7 +0,0 @@ -sample_id,tissue,version,file_scutrquant,file_cellranger -heart_1k_v2_fastq,heart,v2,data/sce/utrome_mm10_v1_fulllength/heart_1k_v2_fastq.genes.Rds,data/counts/heart_1k_v2_filtered_feature_bc_matrix.h5 -heart_1k_v3_fastq,heart,v3,data/sce/utrome_mm10_v1_fulllength/heart_1k_v3_fastq.genes.Rds,data/counts/heart_1k_v3_filtered_feature_bc_matrix.h5 -heart_10k_v3_fastq,heart,v3,data/sce/utrome_mm10_v1_fulllength/heart_10k_v3_fastq.genes.Rds,data/counts/heart_10k_v3_filtered_feature_bc_matrix.h5 -neuron_1k_v2_fastq,neuron,v2,data/sce/utrome_mm10_v1_fulllength/neuron_1k_v2_fastq.genes.Rds,data/counts/neuron_1k_v2_filtered_feature_bc_matrix.h5 -neuron_1k_v3_fastq,neuron,v3,data/sce/utrome_mm10_v1_fulllength/neuron_1k_v3_fastq.genes.Rds,data/counts/neuron_1k_v3_filtered_feature_bc_matrix.h5 -neuron_10k_v3_fastq,neuron,v3,data/sce/utrome_mm10_v1_fulllength/neuron_10k_v3_fastq.genes.Rds,data/counts/neuron_10k_v3_filtered_feature_bc_matrix.h5 diff --git a/metadata/counts_sample_sheet_gencode.csv b/metadata/counts_sample_sheet_gencode.csv deleted file mode 100644 index 710c7ec..0000000 --- a/metadata/counts_sample_sheet_gencode.csv +++ /dev/null @@ -1,7 +0,0 @@ -sample_id,tissue,version,file_scutrquant,file_cellranger -heart_1k_v2_fastq,heart,v2,data/sce/gencode_vM21_w500/heart_1k_v2_fastq.genes.Rds,data/counts/heart_1k_v2_filtered_feature_bc_matrix.h5 -heart_1k_v3_fastq,heart,v3,data/sce/gencode_vM21_w500/heart_1k_v3_fastq.genes.Rds,data/counts/heart_1k_v3_filtered_feature_bc_matrix.h5 -heart_10k_v3_fastq,heart,v3,data/sce/gencode_vM21_w500/heart_10k_v3_fastq.genes.Rds,data/counts/heart_10k_v3_filtered_feature_bc_matrix.h5 -neuron_1k_v2_fastq,neuron,v2,data/sce/gencode_vM21_w500/neuron_1k_v2_fastq.genes.Rds,data/counts/neuron_1k_v2_filtered_feature_bc_matrix.h5 -neuron_1k_v3_fastq,neuron,v3,data/sce/gencode_vM21_w500/neuron_1k_v3_fastq.genes.Rds,data/counts/neuron_1k_v3_filtered_feature_bc_matrix.h5 -neuron_10k_v3_fastq,neuron,v3,data/sce/gencode_vM21_w500/neuron_10k_v3_fastq.genes.Rds,data/counts/neuron_10k_v3_filtered_feature_bc_matrix.h5 diff --git a/metadata/counts_sample_sheet_pbmc.csv b/metadata/counts_sample_sheet_pbmc.csv deleted file mode 100644 index 1d26e7e..0000000 --- a/metadata/counts_sample_sheet_pbmc.csv +++ /dev/null @@ -1,4 +0,0 @@ -sample_id,tissue,version,file_scutrquant,file_cellranger -pbmc_1k_v2_fastq,pbmc,v2,data/sce/ensembl_104_hg38_w500/pbmc_1k_v2_fastq.genes.Rds,data/counts/pbmc_1k_v2_filtered_feature_bc_matrix.h5 -pbmc_1k_v3_fastq,pbmc,v3,data/sce/ensembl_104_hg38_w500/pbmc_1k_v3_fastq.genes.Rds,data/counts/pbmc_1k_v3_filtered_feature_bc_matrix.h5 -pbmc_10k_v3_fastq,pbmc,v3,data/sce/ensembl_104_hg38_w500/pbmc_10k_v3_fastq.genes.Rds,data/counts/pbmc_10k_v3_filtered_feature_bc_matrix.h5 \ No newline at end of file diff --git a/metadata/counts_sample_sheet_pbmc_cr.csv b/metadata/counts_sample_sheet_pbmc_cr.csv deleted file mode 100644 index 5c9aa5c..0000000 --- a/metadata/counts_sample_sheet_pbmc_cr.csv +++ /dev/null @@ -1,4 +0,0 @@ -sample_id,tissue,version,file_scutrquant,file_cellranger -pbmc_1k_v2_fastq,pbmc,v2,data/sce/cellranger_300_hg38_w500/pbmc_1k_v2_fastq.genes.Rds,data/counts/pbmc_1k_v2_filtered_feature_bc_matrix.h5 -pbmc_1k_v3_fastq,pbmc,v3,data/sce/cellranger_300_hg38_w500/pbmc_1k_v3_fastq.genes.Rds,data/counts/pbmc_1k_v3_filtered_feature_bc_matrix.h5 -pbmc_10k_v3_fastq,pbmc,v3,data/sce/cellranger_300_hg38_w500/pbmc_10k_v3_fastq.genes.Rds,data/counts/pbmc_10k_v3_filtered_feature_bc_matrix.h5 \ No newline at end of file diff --git a/metadata/counts_sample_sheet_unfiltered.csv b/metadata/counts_sample_sheet_unfiltered.csv deleted file mode 100644 index d577789..0000000 --- a/metadata/counts_sample_sheet_unfiltered.csv +++ /dev/null @@ -1,7 +0,0 @@ -sample_id,tissue,version,file_scutrquant,file_cellranger -heart_1k_v2_fastq,heart,v2,data/sce/utrome_mm10_v1_unfiltered/heart_1k_v2_fastq.genes.Rds,data/counts/heart_1k_v2_filtered_feature_bc_matrix.h5 -heart_1k_v3_fastq,heart,v3,data/sce/utrome_mm10_v1_unfiltered/heart_1k_v3_fastq.genes.Rds,data/counts/heart_1k_v3_filtered_feature_bc_matrix.h5 -heart_10k_v3_fastq,heart,v3,data/sce/utrome_mm10_v1_unfiltered/heart_10k_v3_fastq.genes.Rds,data/counts/heart_10k_v3_filtered_feature_bc_matrix.h5 -neuron_1k_v2_fastq,neuron,v2,data/sce/utrome_mm10_v1_unfiltered/neuron_1k_v2_fastq.genes.Rds,data/counts/neuron_1k_v2_filtered_feature_bc_matrix.h5 -neuron_1k_v3_fastq,neuron,v3,data/sce/utrome_mm10_v1_unfiltered/neuron_1k_v3_fastq.genes.Rds,data/counts/neuron_1k_v3_filtered_feature_bc_matrix.h5 -neuron_10k_v3_fastq,neuron,v3,data/sce/utrome_mm10_v1_unfiltered/neuron_10k_v3_fastq.genes.Rds,data/counts/neuron_10k_v3_filtered_feature_bc_matrix.h5 diff --git a/numbers/dge-dtu-451lu.Rmd b/numbers/dge-dtu-451lu.Rmd deleted file mode 100644 index 6c41ff3..0000000 --- a/numbers/dge-dtu-451lu.Rmd +++ /dev/null @@ -1,93 +0,0 @@ ---- -title: "DTU vs DGE in 451Lu Data" -author: "Mervin M Fanlser" -date: "`r format(Sys.time(), '%d %B %Y')`" -output: - html_document: - code_folding: show - toc: true - toc_float: true ---- - -# Purpose - -Compare the significant differentially expressed genes to the differential LUI -genes in the *Ho et al., 2018* dataset of 451Lu cells with B-Raf inhibitor -resistance. - -# Initialization - -## Libraries -```{r libs, message=FALSE, warning=FALSE} -library(magrittr) -library(tidyverse) -library(cowplot) -library(org.Hs.eg.db) -``` - -## Parameters -```{r set_params} -set.seed(20210818) -``` - -## Functions - -```{r methods} - -``` - -# Data -## Loading -```{r load_data, message=FALSE} -df_dge <- read_csv("data/dge/Ho18_Supplemental_Table_S3.csv") - -df_dtu <- read_tsv("data/dtu/20211021-451lu-twosample-lui.min50.boot10k.tsv.gz") %>% - mutate(ensembl_id=str_extract(gene, "^[^.]+")) -``` - -## Preprocessing -```{r prepare_data} -df_dtu_filtered <- mapIds(org.Hs.eg.db, df_dtu$ensembl_id, "SYMBOL", "ENSEMBL") %>% - enframe(name="ensembl_id", value="gene_symbol") %>% - full_join(df_dtu, by="ensembl_id") %>% - filter(qval < 0.05, abs(stat) > 0.15) - -df_dge_filtered <- df_dge %>% - filter(padj < 0.05, abs(log2FoldChange) >= 1) -``` - -# Analysis - -## Common Genes - -```{r intersect_genes, fig.width=5, fig.height=4} -intersect(df_dtu_filtered$gene_symbol, df_dge_filtered$Gene) -``` - - -# Conclusion - -It appears there is almost no overlap, however, it is unclear if this gene list -from the SAKE paper is pre-filtered in some way. - ---- - -# Runtime Details -## Session Info -```{r sesh_info, echo=FALSE} -sessionInfo() -``` - -## Conda Environment -```{bash comment="", echo=FALSE} -if ! command -v conda &> /dev/null -then - echo "Conda not detected." -elif [ -z "${CONDA_PREFIX}" ] -then - echo "No active Conda environment." -else - echo "## Conda Environment YAML" - conda env export -fi -``` diff --git a/numbers/dge-dtu-451lu.html b/numbers/dge-dtu-451lu.html deleted file mode 100644 index 430a93d..0000000 --- a/numbers/dge-dtu-451lu.html +++ /dev/null @@ -1,923 +0,0 @@ - - - - - - - - - - - - - - - -DTU vs DGE in 451Lu Data - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - -
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- -
- - - - - - - -
-

Purpose

-

Compare the significant differentially expressed genes to the differential LUI genes in the Ho et al., 2018 dataset of 451Lu cells with B-Raf inhibitor resistance.

-
-
-

Initialization

-
-

Libraries

-
library(magrittr)
-library(tidyverse)
-library(cowplot)
-library(org.Hs.eg.db)
-
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-

Parameters

-
set.seed(20210818)
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Functions

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Data

-
-

Loading

-
df_dge <- read_csv("data/dge/Ho18_Supplemental_Table_S3.csv")
-
-df_dtu <- read_tsv("data/dtu/20211021-451lu-twosample-lui.min50.boot10k.tsv.gz") %>%
-  mutate(ensembl_id=str_extract(gene, "^[^.]+"))
-
-
-

Preprocessing

-
df_dtu_filtered <- mapIds(org.Hs.eg.db, df_dtu$ensembl_id, "SYMBOL", "ENSEMBL") %>%
-  enframe(name="ensembl_id", value="gene_symbol") %>%
-  full_join(df_dtu, by="ensembl_id") %>%
-  filter(qval < 0.05, abs(stat) > 0.15)
-
## 'select()' returned 1:many mapping between keys and columns
-
df_dge_filtered <- df_dge %>% 
-  filter(padj < 0.05, abs(log2FoldChange) >= 1)
-
-
-
-

Analysis

-
-

Common Genes

-
intersect(df_dtu_filtered$gene_symbol, df_dge_filtered$Gene)
-
## [1] "SLC16A6"
-
-
-
-

Conclusion

-

It appears there is almost no overlap, however, it is unclear if this gene list from the SAKE paper is pre-filtered in some way.

-
-
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-

Runtime Details

-
-

Session Info

-
## R version 4.0.2 (2020-06-22)
-## Platform: x86_64-apple-darwin13.4.0 (64-bit)
-## Running under: macOS Mojave 10.14.6
-## 
-## Matrix products: default
-## BLAS/LAPACK: /Users/mfansler/miniconda3/envs/bioc_3_12/lib/libopenblasp-r0.3.10.dylib
-## 
-## locale:
-## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
-## 
-## attached base packages:
-## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
-## [8] methods   base     
-## 
-## other attached packages:
-##  [1] org.Hs.eg.db_3.12.0  AnnotationDbi_1.52.0 IRanges_2.24.0      
-##  [4] S4Vectors_0.28.0     Biobase_2.50.0       BiocGenerics_0.36.0 
-##  [7] cowplot_1.1.0        forcats_0.5.1        stringr_1.4.0       
-## [10] dplyr_1.0.5          purrr_0.3.4          readr_1.4.0         
-## [13] tidyr_1.1.3          tibble_3.1.0         ggplot2_3.3.3       
-## [16] tidyverse_1.3.0      magrittr_2.0.1      
-## 
-## loaded via a namespace (and not attached):
-##  [1] Rcpp_1.0.6        lubridate_1.7.10  assertthat_0.2.1  digest_0.6.27    
-##  [5] utf8_1.1.4        R6_2.5.0          cellranger_1.1.0  backports_1.2.1  
-##  [9] reprex_1.0.0      RSQLite_2.2.3     evaluate_0.14     httr_1.4.2       
-## [13] pillar_1.5.1      rlang_0.4.10      readxl_1.3.1      rstudioapi_0.13  
-## [17] blob_1.2.1        rmarkdown_2.7     bit_4.0.4         munsell_0.5.0    
-## [21] broom_0.7.5       compiler_4.0.2    modelr_0.1.8      xfun_0.20        
-## [25] pkgconfig_2.0.3   htmltools_0.5.1.1 tidyselect_1.1.0  fansi_0.4.2      
-## [29] crayon_1.4.1      dbplyr_2.1.0      withr_2.4.1       grid_4.0.2       
-## [33] jsonlite_1.7.2    gtable_0.3.0      lifecycle_1.0.0   DBI_1.1.1        
-## [37] scales_1.1.1      cachem_1.0.4      cli_2.3.1         stringi_1.5.3    
-## [41] fs_1.5.0          xml2_1.3.2        ellipsis_0.3.1    generics_0.1.0   
-## [45] vctrs_0.3.6       tools_4.0.2       bit64_4.0.5       glue_1.4.2       
-## [49] hms_1.0.0         fastmap_1.1.0     yaml_2.2.1        colorspace_2.0-0 
-## [53] rvest_1.0.0       memoise_2.0.0     knitr_1.31        haven_2.3.1
-
-
-

Conda Environment

-
## Conda Environment YAML
-name: bioc_3_12
-channels:
-  - merv
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - _r-mutex=1.0.1=anacondar_1
-  - _r-xgboost-mutex=2.0=cpu_0
-  - bioconductor-annotate=1.68.0=r40_0
-  - bioconductor-annotationdbi=1.52.0=r40_0
-  - bioconductor-annotationfilter=1.14.0=r40hdfd78af_1
-  - bioconductor-annotationhub=2.22.0=r40_0
-  - bioconductor-apeglm=1.12.0=r40h832b226_1
-  - bioconductor-basilisk=1.2.0=r40_0
-  - bioconductor-basilisk.utils=1.2.0=r40_0
-  - bioconductor-beachmat=2.6.0=r40h64ad5ed_0
-  - bioconductor-biobase=2.50.0=r40h8909d69_0
-  - bioconductor-biocfilecache=1.14.0=r40_0
-  - bioconductor-biocgenerics=0.36.0=r40_0
-  - bioconductor-biocneighbors=1.8.0=r40h64ad5ed_0
-  - bioconductor-biocparallel=1.24.0=r40h64ad5ed_0
-  - bioconductor-biocsingular=1.6.0=r40h64ad5ed_0
-  - bioconductor-biocversion=3.12.0=r40_0
-  - bioconductor-biomart=2.46.0=r40_0
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-prefix: /Users/mfansler/miniconda3/envs/bioc_3_12
-
-
- - - -
-
- -
- - - - - - - - - - - - - - - - - diff --git a/numbers/novel-isoforms.Rmd b/numbers/novel-isoforms.Rmd deleted file mode 100644 index 11153c7..0000000 --- a/numbers/novel-isoforms.Rmd +++ /dev/null @@ -1,90 +0,0 @@ ---- -title: "Isoform Counts" -author: "Mervin M Fansler" -date: "`r format(Sys.time(), '%d %B %Y')`" -output: - html_document: - code_folding: show - toc: true - toc_float: true ---- - -# Purpose - -This document counts the novel isoforms added to the GENCODE annotation. - -# Initialization - -## Libraries -```{r libs, message=FALSE, warning=FALSE} -library(magrittr) -library(tidyverse) -library(plyranges) -``` - -# Data -## Loading -```{r load_data, message=FALSE} -gr_txs <- read_gff2("data/gtf/adult.utrome.e3.t200.f0.999.w500.gtf.gz") %>% - filter(type == 'transcript') -``` - -## Preprocessing -```{r prepare_data} -df_txs <- mcols(gr_txs) %>% - as_tibble %>% - mutate(novel=str_detect(transcript_name, pattern="UTR[-+]"), - upstream=str_detect(transcript_name, pattern="UTR[-]"), - downstream=str_detect(transcript_name, pattern="UTR[+]")) -``` - -# Analysis - -## Novel Transcripts - -```{r tbl_novel, fig.width=5, fig.height=4} -df_txs %>% - count(novel) %>% - knitr::kable() -``` - -## Novel Upstream vs Downstream Transcripts - -```{r tbl_novel_position, fig.width=5, fig.height=4} -df_txs %>% - count(upstream, downstream) %>% - knitr::kable() -``` - -## Genes with Novel Isoforms -```{r tbl_novel_gene} -df_txs %>% - group_by(gene_id) %>% - summarize(has_novel=any(novel), .groups='drop') %>% - count(has_novel) %>% - knitr::kable() -``` - - - ---- - -# Runtime Details -## Session Info -```{r sesh_info, echo=FALSE} -sessionInfo() -``` - -## Conda Environment -```{bash comment="", echo=FALSE} -if ! command -v conda &> /dev/null -then - echo "Conda not detected." -elif [ -z "${CONDA_PREFIX}" ] -then - echo "No active Conda environment." -else - echo "## Conda Environment YAML" - conda env export -fi -``` diff --git a/numbers/novel-isoforms.html b/numbers/novel-isoforms.html deleted file mode 100644 index c3ad12f..0000000 --- a/numbers/novel-isoforms.html +++ /dev/null @@ -1,1004 +0,0 @@ - - - - - - - - - - - - - - - -Isoform Counts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - -
-
-
-
-
- -
- - - - - - - -
-

Purpose

-

This document counts the novel isoforms added to the GENCODE annotation.

-
-
-

Initialization

-
-

Libraries

-
library(magrittr)
-library(tidyverse)
-library(plyranges)
-
-
-
-

Data

-
-

Loading

-
gr_txs <- read_gff2("data/gtf/adult.utrome.e3.t200.f0.999.w500.gtf.gz") %>%
-  filter(type == 'transcript')
-
-
-

Preprocessing

-
df_txs <- mcols(gr_txs) %>%
-  as_tibble %>%
-  mutate(novel=str_detect(transcript_name, pattern="UTR[-+]"),
-         upstream=str_detect(transcript_name, pattern="UTR[-]"),
-         downstream=str_detect(transcript_name, pattern="UTR[+]"))
-
-
-
-

Analysis

-
-

Novel Transcripts

-
df_txs %>%
-  count(novel) %>%
-  knitr::kable()
- - - - - - - - - - - - - - - - - -
noveln
FALSE37014
TRUE9487
-
-
-

Novel Upstream vs Downstream Transcripts

-
df_txs %>%
-  count(upstream, downstream) %>%
-  knitr::kable()
- - - - - - - - - - - - - - - - - - - - - - - - - -
upstreamdownstreamn
FALSEFALSE37014
FALSETRUE922
TRUEFALSE8565
-
-
-

Genes with Novel Isoforms

-
df_txs %>%
-  group_by(gene_id) %>%
-  summarize(has_novel=any(novel), .groups='drop') %>%
-  count(has_novel) %>%
-  knitr::kable()
- - - - - - - - - - - - - - - - - -
has_noveln
FALSE15860
TRUE5931
-
-
-
-
-

Runtime Details

-
-

Session Info

-
## R version 4.0.2 (2020-06-22)
-## Platform: x86_64-apple-darwin13.4.0 (64-bit)
-## Running under: macOS Mojave 10.14.6
-## 
-## Matrix products: default
-## BLAS/LAPACK: /Users/mfansler/miniconda3/envs/bioc_3_12/lib/libopenblasp-r0.3.10.dylib
-## 
-## locale:
-## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
-## 
-## attached base packages:
-## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
-## [8] methods   base     
-## 
-## other attached packages:
-##  [1] plyranges_1.10.0     GenomicRanges_1.42.0 GenomeInfoDb_1.26.4 
-##  [4] IRanges_2.24.0       S4Vectors_0.28.0     BiocGenerics_0.36.0 
-##  [7] forcats_0.5.1        stringr_1.4.0        dplyr_1.0.5         
-## [10] purrr_0.3.4          readr_1.4.0          tidyr_1.1.3         
-## [13] tibble_3.1.0         ggplot2_3.3.3        tidyverse_1.3.0     
-## [16] magrittr_2.0.1      
-## 
-## loaded via a namespace (and not attached):
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-##  [3] httr_1.4.2                  jsonlite_1.7.2             
-##  [5] modelr_0.1.8                assertthat_0.2.1           
-##  [7] highr_0.8                   Rsamtools_2.6.0            
-##  [9] GenomeInfoDbData_1.2.4      cellranger_1.1.0           
-## [11] yaml_2.2.1                  pillar_1.5.1               
-## [13] backports_1.2.1             lattice_0.20-41            
-## [15] glue_1.4.2                  digest_0.6.27              
-## [17] XVector_0.30.0              rvest_1.0.0                
-## [19] colorspace_2.0-0            htmltools_0.5.1.1          
-## [21] Matrix_1.3-2                XML_3.99-0.5               
-## [23] pkgconfig_2.0.3             broom_0.7.5                
-## [25] haven_2.3.1                 zlibbioc_1.36.0            
-## [27] scales_1.1.1                BiocParallel_1.24.0        
-## [29] generics_0.1.0              ellipsis_0.3.1             
-## [31] withr_2.4.1                 SummarizedExperiment_1.20.0
-## [33] cli_2.3.1                   crayon_1.4.1               
-## [35] readxl_1.3.1                evaluate_0.14              
-## [37] fs_1.5.0                    fansi_0.4.2                
-## [39] xml2_1.3.2                  tools_4.0.2                
-## [41] hms_1.0.0                   lifecycle_1.0.0            
-## [43] matrixStats_0.58.0          munsell_0.5.0              
-## [45] reprex_1.0.0                DelayedArray_0.16.0        
-## [47] Biostrings_2.58.0           compiler_4.0.2             
-## [49] rlang_0.4.10                grid_4.0.2                 
-## [51] RCurl_1.98-1.2              rstudioapi_0.13            
-## [53] bitops_1.0-6                rmarkdown_2.7              
-## [55] gtable_0.3.0                DBI_1.1.1                  
-## [57] R6_2.5.0                    GenomicAlignments_1.26.0   
-## [59] lubridate_1.7.10            rtracklayer_1.50.0         
-## [61] knitr_1.31                  utf8_1.1.4                 
-## [63] stringi_1.5.3               Rcpp_1.0.6                 
-## [65] vctrs_0.3.6                 dbplyr_2.1.0               
-## [67] tidyselect_1.1.0            xfun_0.20
-
-
-

Conda Environment

-
## Conda Environment YAML
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