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1,000 results • Page
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0
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5
views
Can someone help me search the minimal value of a two column csv file with a single command or bashscript?
grep
text
csv
10 minutes ago by
mxm189
• 0
0
votes
0
replies
8
views
POSSUM Bioinformatics Tool
BLAST
PSSM
POSSUM
PSI
UNIREF100
20 minutes ago by
Muny
• 0
0
votes
0
replies
7
views
Speciation of insecta using NGS technology
speciation
NGS
18S
insecta
41 minutes ago by
dante
• 0
0
votes
1
reply
52
views
Python Dictionary of Primer3-py Primer Designs
dictionary
primer3-py
python
updated 1 hour ago by
barslmn
★ 1.2k • written 5 hours ago by
bhumm
▴ 10
0
votes
1
reply
31
views
Unable to install clusterProfiler on Mac M1
install
M1
Mac
clusterProfiler
10 minutes ago by
Wang Cong
▴ 10
0
votes
2
replies
59
views
SRA taxonomy analysis
taxonomy
sra
2 hours ago by
Steve
• 0
0
votes
0
replies
26
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
29
views
Lastz align sequence to self in blocks of 1kb
LASTZ
chromosome
self-align
3 hours ago by
polag01
▴ 10
714
votes
159
replies
104k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 months ago by
Biostar
1.5k • written 6.2 years ago by
Istvan Albert
96k
0
votes
1
reply
128
views
scaffold assembly inro chromosomal assembly using reference genome
SCAFFOLD
updated 5 hours ago by
samuel.a.odonnell
▴ 450 • written 21 hours ago by
skdv2522
• 0
0
votes
0
replies
39
views
Find ASVs for Non-Microbial Data
Amplicon
ASV
PCR
BWA
VCF
6 hours ago by
Saran
▴ 10
0
votes
0
replies
39
views
pathwaycommons SPARQL endpoint down?
pathwaycommons
6 hours ago by
mk
▴ 270
3
votes
4
replies
121
views
extracting input files form Seurat
Seurat
Single-Cell
6 hours ago by
rasing02
• 0
0
votes
3
replies
97
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 8 hours ago by
Estefania
▴ 10
2
votes
3
replies
138
views
mirbase does not have miRNA annotation of my species, what are the alternatives?
mirbase
mirna-seq
3 hours ago by
demoraesdiogo2017
▴ 80
0
votes
4
replies
103
views
Getting a VCF file from plink .bed, .fam and .bim files
vcf
plink
4 hours ago by
hi.there
• 0
0
votes
0
replies
39
views
Calculating PRS in a large cohort
PRS
8 hours ago by
haasroni
• 0
0
votes
3
replies
108
views
Downloading 450k methylation data from GEO
minfi
450K
IDAT
Methylation
GEO
updated 6 hours ago by
GenoMax
125k • written 10 hours ago by
Edward E-B
• 0
4
votes
3
replies
95
views
Reads are marked as full of mismatches in IGV, but cigar string shows full length match
cigar
IGV
updated 8 hours ago by
Ram
37k • written 10 hours ago by
jsuzuki
▴ 10
0
votes
0
replies
48
views
seurat: Average expression function and find markers DE fold changes do not add up
Seurat
Single-Cell
updated 8 hours ago by
Ram
37k • written 10 hours ago by
rasing02
• 0
1
vote
0
replies
53
views
Herald:
The Biostar Herald for Monday, January 30, 2023
herald
10 hours ago by
Biostar
1.5k
0
votes
0
replies
43
views
News:
Course - R/Bioconductor for Mass Spectrometry and Proteomics
Bioconductor
MassSpectrometry
R
Proteomics
10 hours ago by
carlopecoraro2
★ 2.2k
0
votes
2
replies
942
views
CNVkit error "pysam.utils.SamtoolsError: "samtools returned with error 2: stdout=, stderr=ERROR: fail to open index BAM file"
software-error
python
cnvkit
updated 8 hours ago by
Ram
37k • written 2.5 years ago by
bgilijia3
• 0
1
vote
2
replies
157
views
How do I remove certain reads from my raw sequencing data using BLAST?
BLAST
updated 10 hours ago by
GenoMax
125k • written 21 hours ago by
yh1126
• 0
0
votes
3
replies
113
views
Help interpreting FastQC report
fastQC
trimming
quality-control
updated 7 hours ago by
GenoMax
125k • written 12 hours ago by
sithlordashley
• 0
0
votes
0
replies
46
views
DepthOfCoverage badly formed genome location error
coverage
12 hours ago by
User000
▴ 620
0
votes
0
replies
37
views
Combination of genomic datasets genotyped using different arrays
genotyping
GWAS
imputation
inflation
12 hours ago by
desicasares
▴ 10
0
votes
2
replies
94
views
Error while using rpy2
R
rpy2
Python
9 hours ago by
sidrah.maryam
▴ 40
0
votes
5
replies
179
views
Issue with VCF format while using Pharmcat
Pharmcat
VCF
updated 12 hours ago by
Pierre Lindenbaum
152k • written 18 hours ago by
taniamahmood38
▴ 20
0
votes
0
replies
40
views
Getting additional positive regulons on enabling --all_modules option in pySCENIC
BioinformaticsTool
Regulon
scRNA-Seq
SCENIC
GRN
pySCENIC
13 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
11
votes
8
replies
19k
views
7 follow
Convert Ensembl Transcript Ids Ensmust To Gene Symbol Using Mygene Module In Python
python
ensembl
convert
gene
updated 14 hours ago by
Francesco
• 0 • written 9.0 years ago by
hicsuntdrac0nis
▴ 240
4
votes
3
replies
5.5k
views
Convert Official Gene Symbols To Uniprot Ids In Python ?
convert
gene
uniprot
python
database
updated 14 hours ago by
Francesco
• 0 • written 8.9 years ago by
hicsuntdrac0nis
▴ 240
1
vote
1
reply
189
views
Biallelicly affected genes in pan cancer tcga data using cbioportal
cBioportal
Biallelic
TCGA
updated 14 hours ago by
pilargmarch
▴ 10 • written 26 days ago by
Camilo Andres
▴ 30
0
votes
8
replies
280
views
blastn (Error: Too many positional arguments (1))
blastn
blast
14 hours ago by
agata
▴ 10
1
vote
2
replies
202
views
How to calculate Minion run time needed?
Minion
updated 14 hours ago by
colindaven
4.4k • written 1 day ago by
ve9
▴ 50
1
vote
1
reply
194
views
cBioportal: Mutations in the database don't appear in the portal
cbioportal
updated 15 hours ago by
pilargmarch
▴ 10 • written 3 days ago by
Camilo Andres
▴ 30
0
votes
0
replies
46
views
Compare population structure results
plots
circlize
dendextend
R
15 hours ago by
waqaskhokhar999
▴ 150
4
votes
6
replies
206
views
nt database Blast
Blast
updated 13 hours ago by
GenoMax
125k • written 17 hours ago by
Giulia.cosenza
▴ 80
0
votes
1
reply
107
views
Mate-pair sequencing
sequecing
sequencing
mate-pair
updated 16 hours ago by
benformatics
3.4k • written 17 hours ago by
Michał
• 0
4
votes
5
replies
294
views
a problem with getBM
getBM
biomart
updated 8 hours ago by
Ram
37k • written 1 day ago by
sanaz
• 0
0
votes
0
replies
89
views
De novo motif in DNA sequences
denovomotif
17 hours ago by
Martina
• 0
0
votes
0
replies
101
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
5
replies
1.0k
views
Structure of an enzyme
enzyme
tissue-specific information
updated 18 hours ago by
fionabingly
• 0 • written 5.2 years ago by
Natasha
▴ 40
25
votes
35
replies
28k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 18 hours ago by
Jan Röslein
▴ 10 • written 8.9 years ago by
komal.rathi
★ 4.0k
0
votes
0
replies
103
views
Gene signature with Machine Learning and Single Cell RNA-seq ?
Cancer
RNA-seq
signature
Cell
Gene
Machine
Learning
Single
19 hours ago by
AKypR
• 0
2
votes
2
replies
416
views
Verify logistic regression assumptions
logistic-regression
updated 8 hours ago by
Ram
37k • written 27 days ago by
AKypR
• 0
0
votes
0
replies
78
views
Use OrthoFinder results in CAFE
expansion
orthofinder
cafe
gene
22 hours ago by
ahmadjoyyia
• 0
2
votes
2
replies
159
views
Annotating snps with gene information
SNPs
gene
annotation
biomart
18 hours ago by
a.wagen
• 0
0
votes
1
reply
213
views
Plink duplicate ID
Plink
updated 1 day ago by
Viktor Messi
• 0 • written 14 days ago by
Aswr
• 0
1,000 results • Page
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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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Recent Replies
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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