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143 results • Page
1 of 3
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0
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0
replies
1
view
Speciation of insecta using NGS technology
speciation
NGS
18S
insecta
just now by
dante
• 0
0
votes
1
reply
25
views
Unable to install clusterProfiler on Mac M1
install
clsuterProfiler
Mac
M1
updated 1 hour ago by
GenoMax
125k • written 1 hour ago by
Wang Cong
▴ 10
0
votes
0
replies
23
views
Error: line 1 did not have 7 elements. --Putting bismark extractor files into methimpute
bioinformatics
RNA-seq
error
next-gen
software
sequence
3 hours ago by
sam
• 0
0
votes
0
replies
26
views
Lastz align sequence to self in blocks of 1kb
LASTZ
chromosome
self-align
3 hours ago by
polag01
▴ 10
0
votes
0
replies
34
views
Find ASVs for Non-Microbial Data
Amplicon
ASV
PCR
BWA
VCF
5 hours ago by
Saran
▴ 10
0
votes
0
replies
36
views
pathwaycommons SPARQL endpoint down?
pathwaycommons
5 hours ago by
mk
▴ 270
0
votes
3
replies
94
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicFeatures
ORFik
GenomicRanges
updated 5 hours ago by
Ram
37k • written 7 hours ago by
Estefania
▴ 10
0
votes
4
replies
100
views
Getting a VCF file from plink .bed, .fam and .bim files
vcf
plink
3 hours ago by
hi.there
• 0
0
votes
0
replies
38
views
Calculating PRS in a large cohort
PRS
7 hours ago by
haasroni
• 0
0
votes
3
replies
105
views
Downloading 450k methylation data from GEO
minfi
450K
IDAT
Methylation
GEO
updated 6 hours ago by
GenoMax
125k • written 9 hours ago by
Edward E-B
• 0
0
votes
0
replies
47
views
seurat: Average expression function and find markers DE fold changes do not add up
Seurat
Single-Cell
updated 7 hours ago by
Ram
37k • written 9 hours ago by
rasing02
• 0
0
votes
3
replies
110
views
Help interpreting FastQC report
fastQC
trimming
quality-control
updated 6 hours ago by
GenoMax
125k • written 11 hours ago by
sithlordashley
• 0
0
votes
0
replies
45
views
DepthOfCoverage badly formed genome location error
coverage
11 hours ago by
User000
▴ 620
0
votes
0
replies
36
views
Combination of genomic datasets genotyped using different arrays
genotyping
GWAS
imputation
inflation
11 hours ago by
desicasares
▴ 10
0
votes
2
replies
93
views
Error while using rpy2
R
rpy2
Python
8 hours ago by
sidrah.maryam
▴ 40
0
votes
0
replies
39
views
Getting additional positive regulons on enabling --all_modules option in pySCENIC
BioinformaticsTool
Regulon
scRNA-Seq
SCENIC
GRN
pySCENIC
12 hours ago by
Nitin Narwade
★ 1.3k
0
votes
0
replies
50
views
SNP data - significance heterozygosity test?
significance
test
SNP
13 hours ago by
Roland
▴ 10
0
votes
0
replies
46
views
Compare population structure results
plots
circlize
dendextend
R
14 hours ago by
waqaskhokhar999
▴ 150
0
votes
0
replies
88
views
De novo motif in DNA sequences
denovomotif
16 hours ago by
Martina
• 0
0
votes
0
replies
99
views
Prediction of SSU, LSU, and ITS regions from genome assembly that related together
ITS
LSU
SSU
16 hours ago by
ALI Hkz
• 0
0
votes
0
replies
101
views
Gene signature with Machine Learning and Single Cell RNA-seq ?
Cancer
RNA-seq
signature
Cell
Gene
Machine
Learning
Single
18 hours ago by
AKypR
• 0
0
votes
0
replies
78
views
Use OrthoFinder results in CAFE
expansion
orthofinder
cafe
gene
21 hours ago by
ahmadjoyyia
• 0
0
votes
1
reply
213
views
Plink duplicate ID
Plink
updated 23 hours ago by
Viktor Messi
• 0 • written 14 days ago by
Aswr
• 0
1
vote
3
replies
169
views
Variant effect predictor in ictalurus punctatus
VariantEffectPredictor
VEP
updated 12 hours ago by
barslmn
★ 1.2k • written 1 day ago by
Hayler Edu
▴ 30
0
votes
2
replies
157
views
merging and annotating bcf files for variant calling
vcf
bcf
calling
bcftools
variant
8 hours ago by
pr.khavari
• 0
0
votes
2
replies
166
views
MesKit error message - Join columns must be present in data.
MesKit
R
4 hours ago by
CH1374
• 0
1
vote
2
replies
164
views
How to install pandas
ml
python
offtopic
updated 7 hours ago by
Ram
37k • written 1 day ago by
Sargun
• 0
0
votes
0
replies
124
views
Scanpy - highest expressed genes
bioinformatics
expressed
normalization
highest
Scanpy
scRNA
genes
1 day ago by
mt_pereira
• 0
0
votes
0
replies
116
views
Normalizing expression values
bioinformatics
logCPM
normalization
Scanpy
scRNA
1 day ago by
mt_pereira
• 0
0
votes
0
replies
133
views
Machine Learning Classifiers on TCGA dataset(tpm_unstrand) gene expression data set
machine
RNASeq
python
learning
1 day ago by
Jakpa
▴ 50
0
votes
0
replies
125
views
getTable ignores query ranges
rtracklayer
1 day ago by
Kyle
• 0
0
votes
0
replies
145
views
maximum fastq file size in galaxy?
fastq
rna-seq
usegalaxy
2 days ago by
demoraesdiogo2017
▴ 80
0
votes
1
reply
198
views
translate CDS to prot formatted with nt nubers
tool
translate
updated 2 days ago by
Pierre Lindenbaum
152k • written 2 days ago by
vvasta
• 0
0
votes
0
replies
188
views
Functional annotation results with Eggnog mapper, For a same query several COGs, several GO:....
COGs
GOs
results
Eggnog
2 days ago by
F.Bedjou
• 0
0
votes
2
replies
239
views
How possible deadlocks are there while migrating from MYISAM to InnoDb?
dbms
updated 2 days ago by
Pierre Lindenbaum
152k • written 2 days ago by
jessewhite8077
• 0
0
votes
0
replies
182
views
How quality score for somatic mutations in ICGC was calculated
somatic
mutations
ICGC
2 days ago by
caochch
• 0
0
votes
0
replies
163
views
vcf2maf - generate 1 maf for 2 vcf files
maf
WES
vcf2maf
updated 7 hours ago by
Ram
37k • written 2 days ago by
CH1374
• 0
0
votes
1
reply
302
views
**Error: unable to open file or unable to determine types for file**
bedtools
updated 2 days ago by
Pierre Lindenbaum
152k • written 2 days ago by
Neel
▴ 10
0
votes
0
replies
185
views
Critical criteria for filtering variants by VariantFiltration
WGS
Filtration
gatk
WES
2 days ago by
Alireza
▴ 20
0
votes
0
replies
179
views
Sc-RNA seq 5’ V2 PE auto detected by CellRanger as R2 only chemistry
cellranger
5prime
PE
R2
V2
2 days ago by
ashley.fletcher2
• 0
0
votes
0
replies
135
views
transcriptome assembly, GWA, BGC
GWA
assembly
BGC
transcriptome
2 days ago by
Kiran
• 0
0
votes
0
replies
223
views
Recommended tools/packages for power and sample size estimation for microRNA gene expression and/or protein expression study?
Power
protein
miRNA
sample
analysis
size
2 days ago by
Lalaland
▴ 10
2
votes
1
reply
238
views
bgzip error 4
bgzip
error4
vcf
updated 2 days ago by
Pierre Lindenbaum
152k • written 3 days ago by
yb
▴ 10
0
votes
1
reply
604
views
pooled-heterozygosity calculation
VCF
Population-Genetics
WGS
Selective-sweep
updated 3 days ago by
mmcui0018
• 0 • written 15 months ago by
reza
▴ 300
0
votes
3
replies
208
views
Help converting .CYCHP to .txt or .csv or .vcf
cychp
updated 3 days ago by
Pierre Lindenbaum
152k • written 3 days ago by
Sarah
• 0
5
votes
13
replies
529
views
How to Calulate Allele Frequency from a VCF File?
frequency
allele
VCF
1 day ago by
Emoji
• 0
0
votes
0
replies
132
views
tximeta accessing gene symbols after addIds()
deseq2
symbols
tximeta
gene
3 days ago by
iddryg
• 0
0
votes
0
replies
135
views
A way to get a list of determined and undetermined indexes using illumina interop library?
interop
python
illumina
updated 7 hours ago by
Ram
37k • written 3 days ago by
fluffycowbird
• 0
1
vote
1
reply
153
views
How to set NCBI entrez to pipe or ignore errors?
NCBI
Entrez
updated 3 days ago by
GenoMax
125k • written 3 days ago by
rijan_dhakal
• 0
1
vote
1
reply
165
views
Aggregate gene expression
AggregateExpression
RNASeq
Seurat
expression
gene
updated 3 days ago by
jv
▴ 760 • written 3 days ago by
Anst
▴ 30
143 results • Page
1 of 3
Recent Votes
Answer: Looking for a tool which provides mapping quality score distributions from BAM f
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: mirbase does not have miRNA annotation of my species, what are the alternatives?
Answer: Gviz python alternative
Answer: Gviz python alternative
Answer: Annotating snps with gene information
Comment: Plotting Correlation matrix
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★ 2.8k
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Answer: Python Dictionary of Primer3-py Primer Designs
by
barslmn
★ 1.2k
You're so close. You can simply loop over sequence dictionaries like you did with the `design_output` and check if the keys with `startswit…
Comment: Unable to install clusterProfiler on Mac M1
by
GenoMax
125k
Have you installed `Xcode` and the command line tools that go with? If not you will need to install those.
Answer: SRA taxonomy analysis
by
Steve
• 0
Thanks @genomax I created an aws glue crawler to pull the data from s3://sra-pub-metadata-us-east-1/sra_tax_analysis_tool/ I wonder if it …
Comment: mirbase does not have miRNA annotation of my species, what are the alternatives?
by
demoraesdiogo2017
▴ 80
thanks! however, shouldn't it also have a gtf/gff file with the annotations?
Comment: Getting a VCF file from plink .bed, .fam and .bim files
by
hi.there
• 0
Thanks Ram. Yes. I have read all of this documentation before. --file and --bfile. I have actually tried doing the complete liftover be…
Answer: SRA taxonomy analysis
by
GenoMax
125k
This data may only be available using `BigQuery` for [**SRA in cloud**][1]. For more information on querying: https://www.ncbi.nlm.nih.g…
Comment: MesKit error message - Join columns must be present in data.
by
CH1374
• 0
column names for the maf are: [1] "Hugo_Symbol" "Chromosome" "Start_Position" [4] "End_Position" "Variant_Classification" "Variant_Type" [7…
Answer: scaffold assembly inro chromosomal assembly using reference genome
by
samuel.a.odonnell
▴ 450
Have a look at ragtag and ragout. I use ragout for smaller assemblies (~20 Mb and less) and ragtag for larger genomes.
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl
by
Ram
37k
I've been meaning to work on a Biostars-specific code formatting manual for a while now but the basic is pretty simple: You can use backtic…
Comment: Multiline Fasta To Single Line Fasta
by
Onur
• 0
Thank you it's also worked for me too. Best,
Comment: CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRl
by
Estefania
▴ 10
Thanks Ram. Could you point to a manual on how to make the post look like yours? I just copy-pasted my R script and this is how it shows in…
Comment: extracting input files form Seurat
by
rasing02
• 0
Thank you jared.andrews07
Comment: extracting input files form Seurat
by
rasing02
• 0
Yes, I just need the input data so that investigators can use tools other than R to visualize the data in form of viloin plots or feature p…
Comment: Downloading 450k methylation data from GEO
by
GenoMax
125k
I don't think they have provided processed data as a single upload.
Answer: extracting input files form Seurat
by
jared.andrews07
★ 14k
You can get the data behind any of the plots easily enough: ``` p <- VlnPlot(Seurat_object, features = "X", group.by = "Names",split.by…
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