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361 results • Page
6 of 8
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
161
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
26 days ago by
rthapa
▴ 90
0
votes
1
reply
161
views
consensus sequence calling
consensus
updated 3 days ago by
bk11
★ 2.5k • written 3 days ago by
Ghada
• 0
0
votes
0
replies
161
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
14 days ago by
Jeyong
• 0
0
votes
1
reply
160
views
How to process Bulk WES data?
WES
WGS
updated 3 days ago by
GenoMax
142k • written 3 days ago by
wyuan37
• 0
1
vote
1
reply
160
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 8 days ago by
andres.firrincieli
3.6k • written 8 days ago by
kacollier
▴ 30
0
votes
1
reply
160
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 3 days ago by
GenoMax
142k • written 3 days ago by
cedric.blais
• 0
0
votes
0
replies
159
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
16 days ago by
O.rka
▴ 720
0
votes
0
replies
158
views
Filter low express genes in microarray data
microarray
19 days ago by
Chris
▴ 280
0
votes
0
replies
157
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 25 days ago by
Ram
43k • written 26 days ago by
sainavyav22
• 0
0
votes
0
replies
157
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
13 days ago by
rustykb
▴ 20
0
votes
0
replies
156
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
26 days ago by
Mamatha Y S
• 0
0
votes
0
replies
156
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
19 days ago by
tnminh89
▴ 10
0
votes
0
replies
156
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
7 days ago by
Samantha
• 0
0
votes
0
replies
155
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 25 days ago by
Carlo Yague
8.7k • written 25 days ago by
Atul K.
• 0
0
votes
1
reply
155
views
input file for alternative splicing in rmats in linux
rmats
updated 7 days ago by
Ram
43k • written 7 days ago by
Lambodarswain316
• 0
1
vote
0
replies
155
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 11 days ago by
zx8754
11k • written 13 days ago by
Emilie
▴ 10
0
votes
0
replies
154
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
7 days ago by
Aytaç
• 0
0
votes
2
replies
153
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
0
votes
0
replies
150
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
17 days ago by
Bine
▴ 60
0
votes
1
reply
149
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 3 days ago by
Ram
43k • written 3 days ago by
eking28
• 0
0
votes
1
reply
148
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 1 day ago by
Michael
54k • written 1 day ago by
mgranada3
▴ 30
0
votes
0
replies
148
views
Empty table plot using plotGseaTable()
FGSEA
13 days ago by
Chris
▴ 280
0
votes
0
replies
147
views
Chance for trained without experience
bio
updated 8 days ago by
ATpoint
82k • written 8 days ago by
shehab
• 0
0
votes
1
reply
146
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 19 hours ago by
GenoMax
142k • written 1 day ago by
Lélé
▴ 10
1
vote
1
reply
145
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
kilcdincer
▴ 10
0
votes
0
replies
144
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
7 days ago by
singcell
• 0
0
votes
0
replies
144
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
17 days ago by
Jacob
• 0
0
votes
1
reply
144
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 22 hours ago by
Papyrus
★ 2.9k • written 1 day ago by
yura.grabovska
▴ 90
0
votes
1
reply
143
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
2 days ago by
sansan_96
▴ 90
0
votes
0
replies
143
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 22 days ago by
Ram
43k • written 23 days ago by
newuser2024
• 0
0
votes
0
replies
143
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
13 days ago by
Javier
• 0
1
vote
0
replies
142
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
8 days ago by
Shae
▴ 10
0
votes
0
replies
140
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
23 days ago by
Kash
▴ 110
0
votes
0
replies
139
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 17 days ago by
dariober
14k • written 19 days ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
138
views
Using limma in methylation EM-seq?
EM-seq
methylation
17 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
136
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
1 day ago by
asalimih
▴ 60
0
votes
0
replies
136
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
13 days ago by
mikemakaveli1
• 0
0
votes
0
replies
136
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 16 days ago by
Ram
43k • written 16 days ago by
Alexandros
• 0
0
votes
0
replies
135
views
Modify plot R mtDNA indel
plot
mtDNA
R
13 days ago by
marco.barr
▴ 120
0
votes
0
replies
134
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
11 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
134
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 15 days ago by
Ram
43k • written 15 days ago by
Oscar
▴ 10
0
votes
1
reply
133
views
Add line under stat test
stats
R
updated 6 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Ghada
• 0
0
votes
0
replies
133
views
Synteny analysis
bacterial
synteny
genome
updated 17 days ago by
GenoMax
142k • written 17 days ago by
Namil
• 0
0
votes
0
replies
129
views
Merging replicates from Encode project
CHIP-seq
encode
23 days ago by
Nurken
• 0
0
votes
0
replies
128
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 24 days ago by
Ram
43k • written 24 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
127
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 23 days ago by
Ram
43k • written 23 days ago by
SHREYA
• 0
0
votes
0
replies
126
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
9 days ago by
Omics data mining
▴ 260
0
votes
0
replies
125
views
How to implement an IGV to streamlit app?
python
streamlit
igv
11 days ago by
avigail.shnaider
• 0
0
votes
0
replies
125
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
11 days ago by
DGTool
▴ 20
0
votes
0
replies
123
views
LEfSe
LEfSe
17 days ago by
benkosta
• 0
361 results • Page
6 of 8
Recent Votes
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
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Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input?
by
Pierre Lindenbaum
161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem
by
Pierre Lindenbaum
161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
DGTool
▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input?
by
LucisTheFather
• 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank you
Comment: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test
by
Nyksubuz
▴ 20
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range
by
Nyksubuz
▴ 20
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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