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Tyler Funnell funnell MSKCC New York

gmcvicker/genome 26

Python library and scripts for retrieval and storage of genomics data in HDF5 format

gmcvicker/draw_genes 13

A flexible python program for generating figures from regions of the genome.

shahcompbio/MultiModalMuSig.jl 11

A Julia package for extracting mutation signatures using topic models

funnell/reactomefi 3

R Reactome FI Cytoscape plugin wrapper

shahcompbio/shahwebsite 2

Shah Lab website source

funnell/vim-config 1

Configuration files for vim

diljotgrewal/shahlab-fortune 0

fortune database of quotes from shahlab members

funnell/awesome-lisp-languages 0

A list of Lisp-flavored programming languages

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Tyler Funnell

commit sha 6c536345b1d349893fd4265f6e7411fe30df906e

increasing heatmap raster resolution (#30)

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Tyler Funnell

commit sha 282e1009e74c8fde402d58e1e61b9e19d9743b39

R-CMD-CHECK workflow installs pandoc (#31)

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Marc Williams

commit sha 20628c005cfb40f0de9930e475e31e80c13980ef

Removing unnecessary functions for bottom annot (#33) * Removing unnecessary functions for bottom annot * Add complexheatmap tag to anno_mark Co-authored-by: Tyler Funnell <tyler.funnell@gmail.com>

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PR opened shahcompbio/schnapps

Removing unnecessary functions for bottom annot

A couple functions were in an early version of the code that were just copied from the ComplexHeatmap package before some fixes could be made to the ComplexHeatmap package itself. Those fixes have been made and so these functions are no longer necessary.

+2 -103

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create barnchfunnell/schnapps

branch : fix-hm-bottom-annot

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PR opened shahcompbio/schnapps

R-CMD-CHECK workflow installs pandoc

R-CMD-CHECK workflow is throwing up errors on my other pull request due to pandoc not being available. Hopefully this fixes that.

+2 -0

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create barnchfunnell/schnapps

branch : fix-r-cmd-check-install-pandoc

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pull request commentshahcompbio/schnapps

increasing heatmap raster resolution

R-CMD-check is complaining about pandoc not being available

funnell

comment created time in 14 days

PR opened shahcompbio/schnapps

increasing heatmap raster resolution

At some point ComplexHeatmap updated how they rasterize heatmaps and this fix makes the heatmaps go from this: image

to this: image

+1 -0

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branch : fix-raster-resolution

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Single Cell Haplotype copy Number Analysis through Phased Probabilistic States

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issue commentSchlossLab/mikropml

Providing case weights

Hi @pschloss, thanks for the reply. I mean, how would I provide the weights argument to the glmnet function. I have unbalanced classes and I'm trying to account for that without down/up-sampling. Thanks for your help!

funnell

comment created time in 2 months

issue openedSchlossLab/mikropml

Providing case weights

Hello,

How would I provide a vector of weights to e.g. glmnet through run_ml?

Thanks!

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Tyler Funnell

commit sha bf6d9ad0a9a85007c9e8e4ee13334c58e600f8e8

old changes

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issue commentropensci/biomartr

EnsemblBacteria: Error: '/tmp/RtmppaSXUW/EnsemblBacteria.txt' does not exist.

I'm able to connect to the server using ftp:

❯ ftp ftp.ncbi.nlm.nih.gov                                                                                                                                                 (base)
Trying 130.14.250.10...
Connected to ftp.ncbi.nlm.nih.gov (130.14.250.10).
220-

can you think of anything else I'd need to check? Thank you very much for your time and help!

ndaniel

comment created time in 3 months

issue commentropensci/biomartr

EnsemblBacteria: Error: '/tmp/RtmppaSXUW/EnsemblBacteria.txt' does not exist.

I have this same problem with the latest version of biomartr. This is happening on a shared compute server.

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /lila/home/funnellt/miniconda3/lib/libopenblasp-r0.3.15.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomartr_1.0.2

loaded via a namespace (and not attached):
 [1] KEGGREST_1.32.0        progress_1.2.2         tidyselect_1.1.1
 [4] remotes_2.4.0          purrr_0.3.4            vctrs_0.3.8
 [7] generics_0.1.0         stats4_4.1.0           BiocFileCache_2.0.0
[10] utf8_1.2.1             blob_1.2.1             XML_3.99-0.6
[13] rlang_0.4.11           pillar_1.6.1           glue_1.4.2
[16] DBI_1.1.1              rappdirs_0.3.3         BiocGenerics_0.38.0
[19] bit64_4.0.5            dbplyr_2.1.1           GenomeInfoDbData_1.2.6
[22] lifecycle_1.0.0        stringr_1.4.0          zlibbioc_1.38.0
[25] Biostrings_2.60.1      memoise_2.0.0          Biobase_2.52.0
[28] IRanges_2.26.0         fastmap_1.1.0          biomaRt_2.48.1
[31] GenomeInfoDb_1.28.0    parallel_4.1.0         curl_4.3.2
[34] AnnotationDbi_1.54.1   fansi_0.5.0            Rcpp_1.0.6
[37] filelock_1.0.2         BiocManager_1.30.16    cachem_1.0.5
[40] S4Vectors_0.30.0       XVector_0.32.0         bit_4.0.4
[43] hms_1.1.0              png_0.1-7              digest_0.6.27
[46] stringi_1.6.2          dplyr_1.0.7            tools_4.1.0
[49] bitops_1.0-7           magrittr_2.0.1         RCurl_1.98-1.3
[52] RSQLite_2.2.5          tibble_3.1.2           crayon_1.4.1
[55] pkgconfig_2.0.3        ellipsis_0.3.2         xml2_1.3.2
[58] prettyunits_1.1.1      assertthat_0.2.1       httr_1.4.2
[61] R6_2.5.0               compiler_4.1.0
ndaniel

comment created time in 3 months

issue commentHomebrew/linuxbrew-core

`ld: cannot find crti.o` error when installing `gcc@5` on CentOS 7

@jacktose what happened to your pull request?

dancooke

comment created time in 3 months