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jtlovell
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GENESPACE
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cannot run orthofinder when activating R4.3 environment using conda
#116
Angelia111
closed
1 year ago
3
Showing smaller contigs
#115
johannesnicolaus
closed
1 year ago
6
Gaps not recognized when building contig map
#114
hanmueller96
closed
1 year ago
1
Riparian plot scale bar color
#113
dmacguigan
closed
1 year ago
1
Understanding non-synteic ortholog
#112
ericgonzalezs
closed
11 months ago
1
Parsing self-formatted BEDs
#111
NatJWalker-Hale
closed
1 year ago
3
Naming convention for block IDs?
#110
Snodgras
closed
1 year ago
1
Plot only secondary hits - Riparian
#109
alexvasilikop
closed
1 year ago
2
Bed file additional field error
#108
SwiftSeal
closed
1 year ago
2
NOTE! Genomes flagged *** have > 5% of genes in over-dispersed orthogroups.
#107
alexvasilikop
closed
1 year ago
2
Documentation for files and their columns in results and other directories
#106
alexvasilikop
closed
1 year ago
4
Difference between physical-position based and gene-rank order based plotting
#105
alexvasilikop
closed
11 months ago
9
Subset ref genome chrs in riparian plot
#104
kushalsuryamohan
closed
1 year ago
1
Is the pangenome not what you are looking for? See figure 1 [here](https://elifesciences.org/articles/78526#content).
#103
xiaoyezao
closed
1 year ago
4
Riparian plot
#102
Ljay4
closed
1 year ago
14
Error in plot_riparian
#101
bbista
closed
1 year ago
2
Genespace docker
#100
sanyalab
closed
1 year ago
8
How to plot region as in Fig 3E in Lovell et al eLife 11:e78526
#99
matt-shenton
closed
1 year ago
3
Stuck at step 3.
#98
theo-allnutt-bioinformatics
closed
1 year ago
4
Reporting a issue for data.table
#97
LQHHHHH
closed
1 year ago
6
Error in rbindlist(mclapply(1:nrow(chnk), mc.cores = nCores, function(i)
#96
theo-allnutt-bioinformatics
closed
1 year ago
7
How to redraw plots outwith a run?
#95
theo-allnutt-bioinformatics
closed
1 year ago
1
Can't find valid path to the MCScanX_h executable
#94
theo-allnutt-bioinformatics
closed
1 year ago
4
segfault upon intialization
#93
jkreinz
closed
1 year ago
8
Riparian plot genome label
#92
JKing2000
closed
1 year ago
3
riparian folder empty after a successful run
#91
YanWangTF
closed
1 year ago
4
Error: subscript contains out-of-bounds indices
#90
YanWangTF
closed
1 year ago
6
Removing unwanted chromosomes from riparian plots
#89
edexter
closed
1 year ago
2
exclude some chromosomes in riparian plotting
#88
xiaoyezao
closed
1 year ago
1
Unspecified WGDs
#87
TommySalvetti01
closed
1 year ago
18
invertTheseChrs available
#86
pascalangst
closed
1 year ago
2
Error in if (is.na(gsParam$synteny$hogs))
#85
xiaoyezao
closed
1 year ago
2
Disk Quota
#84
ericgonzalezs
closed
1 year ago
5
Step 3: Combining and annotating the blast files with orthogroup info error
#83
rac266
closed
1 year ago
4
Error when ignoring multiple genomes
#82
hanneskramml
closed
1 year ago
19
Script stuck at step 3. Combining and annotating the blast files with orthogroup info ...
#81
bbista
closed
1 year ago
19
Error constructing pan-gene sets with sample data
#80
jdobry-lab
closed
1 year ago
8
parsed annotations for ensembl files
#79
rac266
closed
1 year ago
6
parse_annotation
#78
nirwan1265
closed
1 year ago
6
Error in setnames(ogs, c("pgRepID", "ofID")) : Can't assign 2 names to a 0 column data.table
#77
em255
closed
1 year ago
5
Error during `convert_input2v1` and downstream errors without clear error message
#76
pascalangst
closed
1 year ago
7
run_genespace hogs error
#75
SwiftSeal
closed
1 year ago
3
path for diamond
#74
jdobry-lab
closed
1 year ago
2
GENESPACE to infer genome annotation de novo
#73
rodrisenovilla
closed
1 year ago
3
Pangenome order that are not integer.
#72
Jilong-Jerome
closed
1 year ago
2
Memory usage error v1.1.4
#71
peterinnes
closed
1 year ago
2
Step 3 of run_genespace: Item 1 of input is not a data.frame, data.table or list
#70
KaneLab
closed
1 year ago
3
Trouble finding MCScanX
#69
amruta0306
closed
1 year ago
1
Error: In max(hcBlk$rnd1) : no non-missing arguments to max; returning -Inf
#68
timregan
closed
1 year ago
3
ploidy question
#67
dabitz
closed
1 year ago
2
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