Showing : easyrnaseq • reset
1
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2
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2.8k
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mgcv not updating
mgcv easyRNASeq
updated 4.0 years ago by 25k • written 4.0 years ago by ▴ 10
0
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3
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1.5k
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simpleRNASeq easyRNAseq warnings edgeR error
simplernaseq easyrnaseq edger DEformats
updated 7.0 years ago by ▴ 320 • written 7.1 years ago by • 0
4
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5
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1.7k
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Warning: missing reverse strand option in easyRNASeq.
easyrnaseq rnaseq strand
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 10
0
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1
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1.6k
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simpleRNASeq stopped running (related to S4 vectors?)
simplernaseq easyrnaseq s4vectors
updated 9.2 years ago by ▴ 320 • written 9.2 years ago by • 0
0
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2
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1.8k
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Package installation errors for Bioconductor and easyRNASeq
installation biocinstaller easyrnaseq
updated 9.2 years ago by 25k • written 9.2 years ago by • 0
2
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2
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1.7k
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Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error easyrnaseq genomicalignments bam
updated 9.4 years ago by 25k • written 9.4 years ago by ▴ 10
0
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5
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2.6k
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easyRNAseq annotation file
easyrnaseq annotation
9.4 years ago kylvalda • 0
0
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17
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3.3k
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Issue with easyRNASeq
easyRNASeq error
9.6 years ago ea11g0 • 0
1
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13
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3.5k
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Several issues with the package easyRNASeq
easyrnaseq bug
9.6 years ago Michael Dondrup ▴ 10
0
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2
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1.5k
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simpleRNASeq error importing BAM files
simpleRNASeq easyRNASeq
updated 9.6 years ago by 68k • written 9.6 years ago by • 0
0
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6
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2.0k
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easyRNASeq: "Error in IRangesList"
easyRNASeq
9.7 years ago surjray • 0
0
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5
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2.9k
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count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq edger rpkm
updated 10.0 years ago by ▴ 320 • written 10.0 years ago by ▴ 80
2
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6
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2.2k
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easyRNAseq says Your annotation is not in sync with your alignments!
easyRNAseq
updated 10.0 years ago by ▴ 320 • written 10.1 years ago by • 0
0
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1
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3.4k
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easyRNASeq error: Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate
easyrnaseq
10.2 years ago sylvian • 0
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5
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2.4k
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Getting a count matrix from a SummerizedExpriment with EasyRNASeq
easyrnaseq
10.3 years ago Sylvain Foisy ▴ 80
0
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1
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1.3k
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Devel version of easyRNASeq: using the simpleRNASeq method gives an error
easyRNASeq easyRNASeq
updated 10.9 years ago by ▴ 320 • written 10.9 years ago by ▴ 80
0
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2
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1.5k
views
Devel version of easyRNASeq: using the simpleRNASeq method gives an error
Annotation easyRNASeq Annotation easyRNASeq
updated 10.9 years ago by ▴ 80 • written 10.9 years ago by ▴ 320
0
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1
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1.6k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO
updated 11.2 years ago by ▴ 320 • written 11.2 years ago by 52k
0
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1
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2.1k
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Using a countDataSet as input data in DESeq2
easyRNASeq easyRNASeq
updated 11.2 years ago by 43k • written 11.2 years ago by ★ 13k
0
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0
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1.4k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
11.2 years ago Nicolas Delhomme ▴ 320
0
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2
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1.7k
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easyRNAseq and DEseq for no replicate RNAseq
RNASeq PROcess easyRNASeq RNASeq PROcess easyRNASeq
updated 11.2 years ago by ▴ 320 • written 11.2 years ago by ▴ 10
0
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8
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2.3k
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Using easyRNASeq package: question about BAM/BAI and links to them
easyRNASeq easyRNASeq
updated 11.2 years ago by ▴ 80 • written 11.2 years ago by ▴ 80
0
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7
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3.1k
views
GTF file error when using easyRNAseq�
Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq
updated 11.3 years ago by ★ 1.2k • written 11.3 years ago by ★ 13k
0
votes
1
reply
1.5k
views
eayRNASeq with Ensemble GRCh37 help
Annotation Organism easyRNASeq DESeq2 Annotation Organism easyRNASeq DESeq2
updated 11.4 years ago by ★ 1.2k • written 11.4 years ago by ▴ 10
0
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5
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2.0k
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EasyRNAseq - error in building count table - Error in unlist
Sequencing RNASeq edgeR easyRNASeq Sequencing RNASeq edgeR easyRNASeq
updated 11.4 years ago by ★ 1.2k • written 11.4 years ago by ★ 13k
0
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0
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1.4k
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error in "count" for SummarizedExperiment in easyRNASeq
easyRNASeq DESeq2 easyRNASeq DESeq2
11.4 years ago Lescai, Francesco ▴ 380
0
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0
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1.2k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Annotation Organism edgeR DESeq easyRNASeq Annotation Organism edgeR DESeq easyRNASeq
11.7 years ago Gabriele Zoppoli ▴ 50
0
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1
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1.2k
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it is strange that I cannot get the fpkm by using easyRNASeq
Annotation BSgenome BSgenome easyRNASeq Annotation BSgenome BSgenome easyRNASeq
updated 11.9 years ago by ▴ 30 • written 11.9 years ago by ★ 13k
0
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1
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1.6k
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some problems of easyRNASeq� : about the gtf files
Annotation easyRNASeq Annotation easyRNASeq
updated 11.9 years ago by ★ 1.2k • written 11.9 years ago by ★ 13k
0
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0
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1.5k
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RPKM calculation genewise
Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq
12.0 years ago delhomme@embl.de ★ 1.2k
0
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0
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967
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easyRNA adapting annotations to avoid overlapping synthetic exons
Annotation Organism easyRNASeq Annotation Organism easyRNASeq
12.0 years ago delhomme@embl.de ★ 1.2k
0
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0
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1.1k
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easyRNA adapting annotations to avoid overlapping synthetic exons
Annotation Organism easyRNASeq Annotation Organism easyRNASeq
12.0 years ago Bayles, Darrell ▴ 10
0
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0
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1.0k
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easyRNASeq read counts varying when recounting same sample!
Annotation GO biomaRt easyRNASeq Annotation GO biomaRt easyRNASeq
12.0 years ago delhomme@embl.de ★ 1.2k
0
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0
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938
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easyRNASeq read counts varying when recounting same sample!
biomaRt easyRNASeq biomaRt easyRNASeq
12.0 years ago René ▴ 30
0
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1
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1.6k
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Problems in running easyRNASeq
Annotation Organism DEGseq easyRNASeq Annotation Organism DEGseq easyRNASeq
updated 12.1 years ago by ★ 1.2k • written 12.1 years ago by ★ 13k
0
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2
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2.5k
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using easyRNASeq to calculate RPKM values
easyRNASeq easyRNASeq
updated 12.1 years ago by ★ 1.2k • written 12.1 years ago by ▴ 260
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1
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1.4k
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easyRNAseq remove overlapping features
Annotation BSgenome BSgenome IRanges easyRNASeq Annotation BSgenome BSgenome IRanges
updated 12.1 years ago by ★ 1.2k • written 12.1 years ago by ▴ 160
0
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0
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1.7k
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Error message with transcriptCounts(easyRNASeq) performed with gtf file generated with cuffmerge
RNASeq Annotation Normalization Cancer Organism BSgenome BSgenome easyRNASeq RNASeq
12.1 years ago Richard Friedman ★ 2.0k
0
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7
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2.5k
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Getting counts for previously undetected transcripts and genes with easyRNASeq: comparison to Cufflinks
RNASeq Annotation Cancer edgeR cqn easyRNASeq RNASeq Annotation Cancer edgeR cqn
updated 12.2 years ago by ★ 1.2k • written 12.2 years ago by ★ 2.0k
0
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2
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1.4k
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error message with easyRNASeq use case
RNASeq Cancer Organism easyRNASeq RNASeq Cancer Organism easyRNASeq
updated 12.2 years ago by 68k • written 12.2 years ago by ★ 2.0k
0
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1
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1.2k
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easyRNASeq and edgeR
BSgenome BSgenome edgeR easyRNASeq BSgenome BSgenome edgeR easyRNASeq
updated 12.3 years ago by ★ 1.2k • written 12.3 years ago by ★ 13k
0
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3
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2.2k
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Error: 'devel' version requires a more recent R
GUI Cancer easyRNASeq GUI Cancer easyRNASeq
updated 12.3 years ago by 21k • written 12.3 years ago by ★ 2.0k
0
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0
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1.5k
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get synthetic exon dataset with easyRNASeq
RNASeq Alignment Annotation Normalization GO PROcess GenomicRanges DEXSeq easyRNASeq GO
12.3 years ago delhomme@embl.de ★ 1.2k
0
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1
reply
1.5k
views
error in easyRNASeq
RNASeq BSgenome BSgenome easyRNASeq RNASeq BSgenome BSgenome easyRNASeq
updated 12.3 years ago by ★ 1.2k • written 12.3 years ago by ▴ 510
0
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0
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883
views
bam files in sub-directories
easyRNASeq easyRNASeq
12.3 years ago RenéBöttcher ▴ 20
0
votes
1
reply
993
views
bam files in sub-directories
easyRNASeq easyRNASeq
updated 12.3 years ago by ★ 1.2k • written 12.3 years ago by ★ 13k
0
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0
replies
989
views
question on easyRNASeq developer version
GLAD easyRNASeq GLAD easyRNASeq
12.3 years ago delhomme@embl.de ★ 1.2k
0
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0
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1.0k
views
get synthetic exon dataset with easyRNASeq
RNASeq Annotation Normalization GO PROcess easyRNASeq RNASeq Annotation Normalization GO
12.4 years ago delhomme@embl.de ★ 1.2k
0
votes
1
reply
1.0k
views
warnings on easyRNASeq package
Annotation Organism PROcess GenomicRanges easyRNASeq Annotation Organism PROcess
updated 12.4 years ago by ▴ 10 • written 12.4 years ago by ★ 1.2k
0
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2
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1.2k
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RNAseq object
RNASeq DESeq easyRNASeq RNASeq DESeq easyRNASeq
updated 12.4 years ago by ★ 4.2k • written 12.4 years ago by ★ 13k
50 results • Page 1 of 1
Recent ...
Replies
Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies by ATpoint ★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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Teacher to James W. MacDonald 68k
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