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jtlovell
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GENESPACE
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HOG path not getting set?
#163
hyphaltip
closed
3 days ago
3
Step 4 synteny error
#162
Hannah1746
opened
4 days ago
3
run_orthofinder usage issues
#161
xiaoguizz
opened
2 weeks ago
1
Higlighting small region or gene of interest
#160
dmacguigan
opened
1 month ago
5
How to Change Chromosome Shapes or Display Centromeres?
#159
YYsama11
closed
1 month ago
1
Why is it so hard to use GENESPACE?
#158
GurjotSinghSidhu
closed
1 month ago
1
BUG when specifying rawOrthofinderDir
#157
dmacguigan
closed
1 month ago
1
Error in strsplit(id, ",") at step 2
#156
daniilprigozhin
opened
2 months ago
1
Extracting genes used for syntenic blocks
#155
caonetto
closed
1 month ago
1
Issue with Specifying Highlighted Regions in highlightBed
#154
YYsama11
closed
2 months ago
2
Error when running run_genespace
#153
topa92
opened
2 months ago
9
Same gene in multiple orthogroups
#152
jacopoM28
opened
3 months ago
0
How are chromosomes labelled by parse_annotations?
#151
plhm
closed
1 month ago
1
Using fasta (DNA sequences) and gff file from busco genes
#150
KBeine
closed
1 month ago
5
riparian plots are inconsistent
#149
gorliver
closed
1 month ago
2
Error in step 3. Combining and annotating the blast files with orthogroup info ...
#148
htorrado
opened
3 months ago
11
Step 3. 'Combining and annotating blast files'
#147
plhm
closed
1 month ago
3
error in run_genespace
#146
jdobry-lab
closed
3 months ago
2
Could not find a valid path to the orthofinder program from R.
#145
celphin
closed
4 months ago
1
Synteny / homoeologs in polyploids
#144
tallnuttrbgv
closed
1 month ago
3
Parsing error; n unique sequences = 7034, n matched to gff = 0
#143
kcl58759
closed
1 month ago
2
Orthofinder taking very long time
#142
tallnuttrbgv
closed
5 months ago
1
clean_windows docs?
#141
tallnuttrbgv
closed
1 month ago
1
cannot install dependency 'igraph'
#140
tallnuttrbgv
closed
5 months ago
1
Error in if (is.na(gsParam$synteny$hogs)) { : argument is of length zero. when checking orthofinder
#139
cieohsc
closed
5 months ago
1
Error when running init_genespace() on phytozome genomes
#138
samseaver
closed
1 month ago
5
Display chromosomes with no orthologs in riparian plot
#137
AnthonyPiot91
closed
5 months ago
1
Combining and annotating bed files w/ OGs and tandem array info fails
#136
Jadziaa
closed
5 months ago
1
Query Regarding Rerun of OrthoFinder Despite Previous Result Directory Provided
#135
Caoyu819
closed
5 months ago
1
Reading .bed files fails if the .bed file contains more than four columns.
#134
mankiddyman
closed
5 months ago
1
Non-syntenic ortholog is not present in pan-genome table
#133
xiaoyezao
closed
1 month ago
1
riparian plots based on clean_windows output
#132
akautt
closed
5 months ago
1
Plot riparian not the same as dot plots or previous runs of genespace
#131
trm76056
closed
1 month ago
5
Difference between riparian plot plotted in the directory and on console
#130
johannesnicolaus
closed
5 months ago
7
ROI riparian plotting error
#129
aamirwkhan06
closed
5 months ago
1
Question about filtering Diamond results
#128
Hannah1746
closed
7 months ago
5
Highlight the gene of interest across the chromosome
#127
HobbitBaba
closed
7 months ago
2
Error while parsing
#126
gubrins
closed
9 months ago
3
Error in step 3
#125
gubrins
closed
9 months ago
0
installation error
#124
ofedrigo
closed
7 months ago
1
Missing one chromosome on the riparian plot
#123
jacquelinemattos
closed
7 months ago
1
Feature request: automatically minimize number of inversions plotted?
#122
taprs
closed
5 months ago
4
Plot one chromosome and highlight regions on it?
#121
ericgonzalezs
closed
1 month ago
7
clean_windows() dotplot has swapped X Y axis title
#120
JKing2000
closed
9 months ago
1
Plot_Riparian error during run_genespace
#119
nhartwic
closed
7 months ago
3
Question about changes in synteny when adding more genomes
#118
JKing2000
closed
7 months ago
3
Error in `[.data.table`(bedm, , `:=`(reford, (1:.N)/.N), by = "genome")
#117
Sidduppal
closed
11 months ago
1
cannot run orthofinder when activating R4.3 environment using conda
#116
Angelia111
closed
11 months ago
3
Showing smaller contigs
#115
johannesnicolaus
closed
11 months ago
6
Gaps not recognized when building contig map
#114
hanmueller96
closed
12 months ago
1
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