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310 results • Page
3 of 7
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Votes
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0
votes
0
replies
130
views
Install packages in old version Julia
package
Julia
18 days ago by
sooni
▴ 10
0
votes
0
replies
140
views
maftools - median survival time doesn't match plot
R
survival
maftools
K-M
11 days ago by
BioGuy
• 0
0
votes
2
replies
303
views
NCBI Genome Workbench Sequence ID edit
NCBI
Workbench
Genome
Sequence
24 days ago by
Paige
• 0
0
votes
0
replies
169
views
Polishing unicycler hybrid assembly results
hybrid
unicycler
polish
27 days ago by
YAYA
• 0
0
votes
1
reply
229
views
Biopython and Fab detection
biopython
fab-detection
antibody
updated 29 days ago by
Jesse
▴ 720 • written 4 weeks ago by
PamCraven
• 0
0
votes
0
replies
171
views
Current landscape of approaches to scRNA-seq with nanopore sequencers?
scRNA-seq
nanopore
single-cell
5 days ago by
LauferVA
3.7k
0
votes
3
replies
324
views
RdRp scan - identifying/detecting viruses- metagenomic workflow- need help
RdRp
virus-detection
metagenomic
updated 11 days ago by
Ram
40k • written 15 days ago by
eric--carron
• 0
0
votes
3
replies
2.0k
views
extraction of original gene iDs from reference annotation file
rna-seq
updated 10 days ago by
aishwarya
• 0 • written 5.3 years ago by
blooming.daisy333
▴ 110
0
votes
1
reply
181
views
PyMOL: how to list all selection names?
pymol
updated 11 days ago by
Wayne
★ 1.8k • written 12 days ago by
Ondina
▴ 90
0
votes
0
replies
210
views
Tools to turn perfect phylogenetic matrix into a tree
parsimony
Phylogeny
tree
14 days ago by
Ritu_K
▴ 10
0
votes
0
replies
175
views
Help with scvi error
scvi
updated 22 days ago by
Ram
40k • written 22 days ago by
Chris
▴ 200
0
votes
3
replies
331
views
Not all variants are annotated with AF - expected or a problem?
Alignment
WGS
Calling
Variant
updated 22 days ago by
GenoMax
134k • written 22 days ago by
Luiz
▴ 30
0
votes
1
reply
307
views
how to determine n_cells_by_count
scanpy
updated 15 days ago by
yl759
▴ 40 • written 12 weeks ago by
dalibenam64
• 0
0
votes
0
replies
135
views
Issue in creating Gene Regulatory Network links using CellOracle
Python
CellOracle
GRN
14 days ago by
Debashish
• 0
0
votes
2
replies
384
views
log2fC from limma on methylation analysis
methylation
limma
minfi
fold-change
updated 14 days ago by
Ram
40k • written 11 months ago by
adeizadavid
▴ 10
0
votes
0
replies
130
views
Implementing covariates in calculating differential methylation
rrbs
methylkit
epigenomics
25 days ago by
Srinka
▴ 20
0
votes
0
replies
206
views
External validation in bioinformatics analyses
External
validation
15 days ago by
Saeedeh Salehi
▴ 10
0
votes
0
replies
190
views
TCGAbiolinks not working anymore
R
TCGAbiolinks
GDC
updated 21 days ago by
Ram
40k • written 21 days ago by
master chief
• 0
0
votes
0
replies
152
views
Find reference genome regions spanned by only mapping quality 0 reads in multiple WGS samples
mapping-quality
BAM
FASTA
26 days ago by
William
★ 5.2k
0
votes
0
replies
138
views
rDNA copy number variation (CNV) based on hg38
hg38
CNVkit
rDNA
CNV
genomics
16 days ago by
rbioinfo
▴ 10
0
votes
1
reply
177
views
vg rna pantranscriptome
rna
vg
updated 10 days ago by
Jordan M Eizenga
▴ 360 • written 11 days ago by
z
• 0
0
votes
0
replies
108
views
RepeatMasker format in SQuIRE Fetch
SQuIRE
RepeatMasker
updated 24 days ago by
Ram
40k • written 24 days ago by
Javier
• 0
0
votes
1
reply
270
views
WGCNA
WGCNA
Degree
igraph
updated 27 days ago by
LauferVA
3.7k • written 27 days ago by
Mehwish
▴ 10
0
votes
2
replies
248
views
Segmentation fault error in CONTROL-FREEC
copy-number-variants
FREEC
18 days ago by
DdogBoss
• 0
0
votes
1
reply
188
views
Drawing label around clusters
cells
Single
updated 18 days ago by
Mensur Dlakic
★ 25k • written 18 days ago by
synat.keam
▴ 80
0
votes
2
replies
293
views
miRNAseq - over-presented sequence in negative control
miRNAseq
adaptor
dimer
18 days ago by
MH85
• 0
0
votes
0
replies
125
views
RnBeads Differential Methylation
rnbeads
RNA-seq
methylation
updated 24 days ago by
Ram
40k • written 25 days ago by
aroso491
• 0
0
votes
2
replies
241
views
Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?
scrna-seq
rna-seq
log2fc
9 days ago by
JLee
• 0
0
votes
0
replies
126
views
assembly: purge_dups removes too much sequence
purge_dups
assembly
nanopore
repeats
plants
16 days ago by
colindaven
5.5k
0
votes
1
reply
139
views
DESeq2 error - converting result object into dataframe
R
DESeq2
Shiny
updated 3 days ago by
Ram
40k • written 3 days ago by
shasabhi1
• 0
0
votes
2
replies
301
views
ClusterProfiler GeneRatio demoninator not the same for all values
enrichment-analysis
clusterprofiler
RNA-seq
deseq2
23 days ago by
Lily
• 0
0
votes
3
replies
177
views
Bug of vg surject
vg
updated 3 days ago by
Jordan M Eizenga
▴ 360 • written 3 days ago by
Qi
• 0
0
votes
0
replies
185
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
9 days ago by
juliviglino
• 0
0
votes
0
replies
124
views
How to compare degradation rate or half-life
degradation-rate
half-life
updated 23 days ago by
Ram
40k • written 23 days ago by
g744695539
• 0
0
votes
0
replies
171
views
Density plot for Quantile and Quartile normalization in geomx workflow
GeoMX
workflow
28 days ago by
Nai
▴ 50
0
votes
3
replies
290
views
Extracting/assembling organellar reads from RNAseq data
transcriptome
star
alignment
mapping
updated 11 days ago by
LChart
3.4k • written 18 days ago by
Miles
• 0
0
votes
0
replies
55
views
rMats Run Does Not Generate More Than One Output Row Per File
Singularity
rMats
sif
14 hours ago by
Y
• 0
0
votes
0
replies
119
views
[Protein-Protein Interaction Network][STRING DB]
proteome
PPI
bacteria
Network
19 days ago by
amresharma1
• 0
0
votes
1
reply
123
views
Running Ibex on both BCR chains?
BCR
ibex
single-cell
updated 4 days ago by
Ram
40k • written 5 days ago by
actinia94
• 0
0
votes
0
replies
120
views
How to annotate BED for tissue expression?
BED
annotation
4 days ago by
Fabio_bie88
• 0
0
votes
0
replies
133
views
Genetic distance in cM from VCF of non-reference species to run Beagle
plink
beagle
vcf
updated 10 days ago by
Ram
40k • written 11 days ago by
AndrMod
• 0
0
votes
1
reply
1.7k
views
error when running local chlorop1.1
chlorop
updated 4 days ago by
Ram
40k • written 7.3 years ago by
gerrychang1985
▴ 40
0
votes
2
replies
691
views
RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
genomics
transcriptome
rsem
ngs
2 days ago by
kat.bi
• 0
0
votes
0
replies
101
views
Guide for ICD-10 to EFO conversion?
icd10
efo
2 days ago by
optimistsso4co3
▴ 100
0
votes
0
replies
95
views
How to obtain de pvalue of my DMRs using Bumphunter function from minfi
DMRs
2 days ago by
Irene
• 0
0
votes
1
reply
252
views
How to predict/annotate whether some type strains has a certain type of enzyme?
genome
gene
blast
annotation
updated 21 days ago by
GenoMax
134k • written 21 days ago by
JyiYeung
• 0
0
votes
4
replies
634
views
CAZy database has multiple family sequence...
metagenomics
cazy
annotation
updated 23 days ago by
JyiYeung
• 0 • written 9 months ago by
GYUDAE
• 0
0
votes
0
replies
135
views
Cluster files from 2018-2020 archive of PDB
database
PDB
archive
Structural
17 days ago by
yhdist
▴ 70
0
votes
0
replies
157
views
simuations with sim1000g
snps
simulation
sim1000G
chromosome
21 days ago by
Eliza
▴ 30
0
votes
0
replies
153
views
Differential expression between two different species tomato and pepper
Differential-expression
updated 29 days ago by
Ram
40k • written 4 weeks ago by
Amior
• 0
310 results • Page
3 of 7
Recent Votes
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
Comment: ncbi error report log for validate fastq issue
A: Bowtie2 MAPQ difference using local vs end-to-end alignment
C: Bowtie2 MAPQ difference using local vs end-to-end alignment
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Recent Replies
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output
by
langziv
▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
by
Pierre Lindenbaum
157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Comment: Subclustering of intergated cells from scRNA-seq data
by
fifty_fifty
▴ 60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names?
by
Mensur Dlakic
★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Ram
40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools
by
Amitm
★ 2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
• 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
This is a really neat package, but I don't think it does exactly what I want, so I've clarified my question. This seems like it grabs a PD…
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