User: ChIP-Tease

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ChIP-Tease0
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Posts by ChIP-Tease

<prev • 12 results • page 1 of 2 • next >
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Questions about Pathview, maybe also gage
... Hello everybody, Today i found the R Pathview package and could already produce some output pictures. Nevertheless i have some problems and hope that someone might help me out. 1. There is a difference between the original KEGG picture and the modified Pathview picture.    I guess this is not supp ...
gage pathview R written 16 months ago by ChIP-Tease0 • updated 11 months ago by bioinf0
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Comment: C: DESeq2 color coding
... Thanks a lot, that helped a lot! ...
written 18 months ago by ChIP-Tease0
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DESeq2 color coding
... Hello everybody, i was wondering, if it is possible to change the color coding in the DESeq2 plotMA function? Since i cannot see how the function works, i don't know how to modify anything. Additionally i would like to see how the plotMA works, which points to the same problem: I cannot see any c ...
deseq2 color r package written 18 months ago by ChIP-Tease0 • updated 18 months ago by Mike Smith2.1k
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Comment: C: How to automate a process on the command line for 1500 genes?
... Hello Jim, Thanks a lot! I accepted it. I didn't know so far that i can accept answers. Also thanks for that hint ...
written 2.3 years ago by ChIP-Tease0
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Answer: A: How to automate a process on the command line for 1500 genes?
... Hello everybody, i cannot really make this suggestion work. for file in *gff;do gene=${${file##aa_bb_cc_dd_}%.gff} echo program.sh $file ../../../unchanged_file.txt $gene $file $gene.bed done The problem seems to be this part: gene=${${file##aa_bb_cc_dd_}%.gff} I understand that the $ ...
written 2.3 years ago by ChIP-Tease0
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Comment: C: How to automate a process on the command line for 1500 genes?
...  Thank you! ...
written 2.3 years ago by ChIP-Tease0
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Comment: C: How to automate a process on the command line for 1500 genes?
... Thanks a lot, i didn't know that R can call command line programs. This will be very usefull for me. I guess i will try both ways. Thanks a lot again! ...
written 2.3 years ago by ChIP-Tease0
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How to automate a process on the command line for 1500 genes?
... Hello everybody,   I have a problem i need some help for. When I run a program on the command line for a single gene, it works fine: program.sh genename_1 ../../../unchanged_file.txt ../../aa_bb_cc_dd_genename_1.gff genename_1.bed   But I need to run it about 1500 times on the command line and ...
command line automation loop written 2.3 years ago by ChIP-Tease0
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Answer: A: Delete all rows which contain a GeneID from a list with several GeneIDs
... Thanks Jeremy, works perfectly, exactly what i was looking for :D ...
written 2.4 years ago by ChIP-Tease0
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Delete all rows which contain a GeneID from a list with several GeneIDs
... Hello everybody, maybe someone has an idea how to solve my problem. I have a data frame and it contains all GeneIDs and a value for these genes. Like this: all_genes (around 23000 rows) GeneID Value Gene1 4 Gene2 2 Gene3 9 Gene4 0 ...
R written 2.4 years ago by ChIP-Tease0

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