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What R/Bioconductor tools would you recommend for the analysis of sncRNA, specifically piRNA?
Bioconductor
updated 2 days ago by ★ 4.0k • written 5 weeks ago by ▴ 380
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563
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Comment: Comment: Does anyone have the command to download all of the core_nt using blast_db_get()
8 months ago Matthew Thornton ▴ 380
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1
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563
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Does anyone have the command to download all of the core_nt using blast_db_get()
rBLAST BiocFileCache
updated 8 months ago by 4.2k • written 8 months ago by ▴ 380
0
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0
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672
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Comment: Comment: Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment
15 months ago Matthew Thornton ▴ 380
0
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1
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672
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Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment
seqFISH SpatialExperiment
15 months ago Matthew Thornton ▴ 380
2
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2
replies
1.2k
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Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
18 months ago Matthew Thornton ▴ 380
2
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0
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1.2k
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Answer: Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
18 months ago Matthew Thornton ▴ 380
0
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1
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2.0k
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Comment: Comment: GOstats - subsetting termGraphs with terms from the html report and missing node
2.7 years ago Matthew Thornton ▴ 380
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1
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2.0k
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Comment: Comment: GOstats - subsetting termGraphs with terms from the html report and missing node
2.7 years ago Matthew Thornton ▴ 380
0
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1
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2.0k
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Comment: Comment: GOstats - subsetting termGraphs with terms from the html report and missing node
2.7 years ago Matthew Thornton ▴ 380
0
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1
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2.0k
views
Comment: Comment: GOstats - subsetting termGraphs with terms from the html report and missing node
2.7 years ago Matthew Thornton ▴ 380
1
vote
9
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2.0k
views
GOstats - subsetting termGraphs with terms from the html report and missing nodes
GOstats
updated 2.7 years ago by • 0 • written 2.7 years ago by ▴ 380
1
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1
reply
1.8k
views
Comment: Comment: DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use D
3.6 years ago Matthew Thornton ▴ 380
1
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0
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4.9k
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Comment: Comment: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
3.6 years ago Matthew Thornton ▴ 380
0
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0
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4.9k
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Comment: Comment: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
3.6 years ago Matthew Thornton ▴ 380
0
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0
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4.9k
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Comment: Comment: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
3.6 years ago Matthew Thornton ▴ 380
8
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12
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4.9k
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DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
DEXSeq
updated 17 months ago by ▴ 30 • written 3.6 years ago by ▴ 380
0
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2
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4.9k
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Comment: Comment: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
3.6 years ago Matthew Thornton ▴ 380
0
votes
1
reply
4.9k
views
Comment: Comment: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
3.6 years ago Matthew Thornton ▴ 380
0
votes
1
reply
4.9k
views
Comment: Comment: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
3.6 years ago Matthew Thornton ▴ 380
0
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0
replies
2.0k
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Comment: Comment: ensembldb to make the EnsDb for Human Version 105 using 'fetchTablesFromEnsembl'
3.7 years ago Matthew Thornton ▴ 380
2
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2
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2.0k
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ensembldb to make the EnsDb for Human Version 105 using 'fetchTablesFromEnsembl' I'm on day two, can it be sped up?
ensembldb
3.7 years ago Matthew Thornton ▴ 380
1
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1
reply
5.7k
views
Processing Nanostring GeoMX Q3 normalized data as intensities with Limma
Limma GeoMX
updated 4.2 years ago by • 0 • written 4.4 years ago by ▴ 380
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0
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631
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CAMTHC with RPKMs giving a very low cluster number than expected
CAMTHC
6.0 years ago Matthew Thornton ▴ 380
1
vote
0
replies
2.0k
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Answer: A: Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differi
6.5 years ago Matthew Thornton ▴ 380
3
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4
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2.0k
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Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differing number of rows'
RCy3 Cytoscape Rgraphviz GOstats
6.5 years ago Matthew Thornton ▴ 380
0
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0
replies
2.0k
views
Comment: C: Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differi
6.5 years ago Matthew Thornton ▴ 380
0
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0
replies
2.0k
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Comment: C: Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differi
6.5 years ago Matthew Thornton ▴ 380
0
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0
replies
2.5k
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Comment: C: Combining and using 10x Genomics output in SingleCellExperiment Objects
6.6 years ago Matthew Thornton ▴ 380
1
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3
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2.5k
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Combining and using 10x Genomics output in SingleCellExperiment Objects
SingleCellExperiment
written 6.6 years ago by ▴ 380
0
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0
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1.8k
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Answer: A: Segmentation Fault with development versions of R, Bioconductor, and DropletUtil
6.6 years ago Matthew Thornton ▴ 380
1
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2
replies
1.8k
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Segmentation Fault with development versions of R, Bioconductor, and DropletUtils when processing output of CellRanger 3.0.2
DropletUtils Bioc-devel
6.6 years ago Matthew Thornton ▴ 380
0
votes
4
replies
2.6k
views
Error importing molecule_info.h5 file generated by Cell Ranger 3.0.2 into DropletUtils
DropletUtils h5
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 380
0
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1
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2.6k
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Comment: C: Error importing molecule_info.h5 file generated by Cell Ranger 3.0.2 into Drople
6.6 years ago Matthew Thornton ▴ 380
0
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0
replies
2.6k
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Comment: C: Error importing molecule_info.h5 file generated by Cell Ranger 3.0.2 into Drople
6.6 years ago Matthew Thornton ▴ 380
0
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0
replies
6.9k
views
Comment: C: What are the methods to get count data per cell from single cell fastq given onl
6.6 years ago Matthew Thornton ▴ 380
0
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0
replies
6.9k
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Comment: C: What are the methods to get count data per cell from single cell fastq given onl
6.6 years ago Matthew Thornton ▴ 380
0
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0
replies
6.9k
views
Comment: C: What are the methods to get count data per cell from single cell fastq given onl
6.7 years ago Matthew Thornton ▴ 380
0
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0
replies
6.9k
views
Comment: C: What are the methods to get count data per cell from single cell fastq given onl
6.7 years ago Matthew Thornton ▴ 380
7
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7
replies
6.9k
views
What are the methods to get count data per cell from single cell fastq given only R1, R2, and I1 fastq files
fastq single cell
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 380
1
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1
reply
1.7k
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Comment: C: DEXSeqHTML and biomart object
7.6 years ago Matthew Thornton ▴ 380
0
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0
replies
1.3k
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Comment: C: Annotation of DEXSeqHTML with biomaRt
7.6 years ago Matthew Thornton ▴ 380
0
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1
reply
1.3k
views
Comment: C: Annotation of DEXSeqHTML with biomaRt
7.6 years ago Matthew Thornton ▴ 380
0
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4
replies
1.3k
views
Annotation of DEXSeqHTML with biomaRt
dexseq biomart
7.6 years ago Matthew Thornton ▴ 380
0
votes
0
replies
1.4k
views
Figuring out what long decent Phred value unaligned reads are
rnaseq alignment
9.0 years ago Matthew Thornton ▴ 380
0
votes
2
replies
1.6k
views
xps - error in normalize - "Error: Length of non-varying units is zero."
Normalization PROcess xps Normalization PROcess xps
updated 11.3 years ago by ★ 3.9k • written 11.3 years ago by ▴ 380
0
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0
replies
1.9k
views
Comment: C: External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??
11.4 years ago Matthew Thornton ▴ 380
0
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3
replies
1.9k
views
External RNA controls on Rat Gene ST 2.0 chip lfc ~ 1 after xps rma??
Normalization xps Normalization xps
updated 11.4 years ago by ▴ 350 • written 11.4 years ago by ▴ 380
0
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1
reply
1.6k
views
VSN with spike-in probes question
vsn vsn
updated 11.4 years ago by ★ 13k • written 11.4 years ago by ▴ 380
3
votes
4
replies
4.9k
views
What is the easiest way to make the GC content and length matrix for package cqn?
RNASeq edgeR cqn RNASeq edgeR cqn
updated 11.6 years ago by 25k • written 11.6 years ago by ▴ 380
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