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119,957 results • Page
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0
votes
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13
views
"Unable to establish SSL connection" error for downloadin in wsl ubuntu by wget
ubuntu
wget
ssl
HISAT2
linux
50 minutes ago by
ali.kian.saei
▴ 10
0
votes
0
replies
35
views
making a circos for snps indels and SV
circos
4 hours ago by
analyst
▴ 50
0
votes
1
reply
129
views
Compute P-Values for SNP Fst from Pairwise Fst Calculations (--weir-fst-pop)
SNP
Analysis
Calculation
Pairwise
VCFtools
Fst
P-value
Calculations
updated 5 hours ago by
Jorge Amigo
14k • written 1 day ago by
Armin
▴ 10
0
votes
2
replies
262
views
chip seq data visualization
macs2
bamcompare
bdgcomp
deeptools
chip-seq
6 hours ago by
nswati106
• 0
0
votes
0
replies
48
views
ssGSEA & WGCNA workflow approach
ssGSEA
WGCNA
6 hours ago by
TNF_alpha
• 0
825
votes
169
replies
162k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
3.3k • written 8.1 years ago by
Istvan Albert
102k
0
votes
0
replies
57
views
PanSN naming issue in pggb fastas
PanSN
pggb
13 hours ago by
Whirlingdaf
▴ 60
4
votes
4
replies
217
views
Create the correct contrast in limma when want to combine 2 or more groups
contrast
limma
DEA
6 hours ago by
Lila M
★ 1.3k
0
votes
0
replies
67
views
Biomart doesn't output ALL uniprot IDs
biomart
Uniprot
18 hours ago by
sgupt46
• 0
1
vote
4
replies
253
views
cant import VCF into OneMap, read.vcfR works but onemap_read_vcfR doesn't
R
onemap
vcf
vcfR
updated 19 hours ago by
Michael
55k • written 1 day ago by
dimeresia
• 0
0
votes
1
reply
198
views
cellxgene DNA Methylation data
cellxgene
updated 21 hours ago by
LChart
4.7k • written 2 days ago by
1769mkc
★ 1.2k
3
votes
6
replies
351
views
How to check for adapters?
Adapters
trimmomatic
ngs
updated 16 hours ago by
GenoMax
148k • written 2 days ago by
Luna
• 0
0
votes
2
replies
163
views
TCGA miRNA data query
tcga
mirna
8 hours ago by
jain72744
▴ 10
0
votes
0
replies
90
views
TCGA -LIHC Isoform Expression Data
isoform
tcga
1 day ago by
jain72744
▴ 10
2
votes
1
reply
323
views
is there any possible way I can tell whether the presence of more bands in the elutions are because of insufficient washing or truncated/degraded pro…
protein
purification
offtopic
updated 1 day ago by
GenoMax
148k • written 1 day ago by
mohammed
• 0
0
votes
1
reply
226
views
Recommended reliable enrichment tool
ontology
enrichr
enrichment
updated 1 day ago by
EagleEye
7.6k • written 3 days ago by
noamizc
• 0
0
votes
1
reply
168
views
MFE in RNA structure
RNA
updated 1 day ago by
Mensur Dlakic
★ 28k • written 2 days ago by
Ebtihal
• 0
0
votes
1
reply
186
views
nf-core/sarek pipeline : adding genome index in config file
nf-core
config
memory
variantcalling
sarek
updated 2 days ago by
Maxime Garcia
▴ 350 • written 2 days ago by
ashaneev07
▴ 50
0
votes
1
reply
178
views
N content - Sequence Quality
fastp
fastq
preprocessing
WGS
updated 1 day ago by
GenoMax
148k • written 2 days ago by
j.k3096
• 0
1
vote
1
reply
219
views
Seeking Explanation for the "Secondbest" Method in Gene log2FC Calculations with CRISPR Data in MAGeCK
CRISPR
log2FC
analysis
mageck
gene
updated 2 days ago by
ATpoint
86k • written 2 days ago by
yanbinwan
• 0
0
votes
1
reply
438
views
What is the proper output for a psiclass_vote.gtf file, and how does one add gene names and strand to gtf files?
psiclass
RNA-seq
2 days ago by
DdogBoss
▴ 20
0
votes
3
replies
703
views
cellranger error fix GTF
gtf
cellranger
scRNA-seq
updated 3 days ago by
ljhgege
• 0 • written 6 months ago by
marco.barr
▴ 160
0
votes
1
reply
217
views
Commands for processing mixed 4-sample scRNA-seq data with cellranger
Cellranger
scRNA-seq
Chromium
updated 3 days ago by
ATpoint
86k • written 3 days ago by
Apprentice
▴ 170
0
votes
0
replies
182
views
Forum:
Survey: Exploring RNA Data Quality in Genomics
Quality
Interpretation
Sequencing
Survey
RNA
15 hours ago by
chrisk
• 0
11
votes
12
replies
884
views
6 follow
Forum:
New Macbook M4 laptops (Pro vs Max)
Pro
Max
Mac
RNA-Seq
M4
updated 2 days ago by
dsull
★ 7.1k • written 4 days ago by
tommygoe
• 0
0
votes
2
replies
340
views
miRBase is down
miRBase
2 days ago by
tyron.chang
• 0
0
votes
0
replies
261
views
miRNA-seq Analysis: Is a low percentage of assigned reads normal when using a miRBase gff file for counting
miRNA
Counting
RNAseq
4 days ago by
Sib
▴ 60
0
votes
3
replies
400
views
Does anyone know how to transform the following transcript ID's from TCGA isoform data
UCSC
isoform
TCGA
updated 2 days ago by
Maximilian Haeussler
★ 1.7k • written 4 days ago by
B.N.
▴ 10
0
votes
1
reply
233
views
Sample-wise raw count matrix from 10x multiplexed data
cellranger
soupx
singlecellRNASeq
10X
updated 4 days ago by
ATpoint
86k • written 4 days ago by
AB
▴ 360
3
votes
1
reply
297
views
How to Test Statistical Association Between Clusters and Conditions in scRNA-seq Data?
scRNA-seq
updated 5 days ago by
jared.andrews07
★ 18k • written 5 days ago by
fifty_fifty
▴ 70
0
votes
1
reply
279
views
GATK is throwing an error when using dbsnp hg19 or GCRCh 38 build 156
and
dnsp156.40
dbsnp
build156.25
updated 5 days ago by
Pierre Lindenbaum
164k • written 5 days ago by
Karibu
• 0
3
votes
3
replies
500
views
Cattle reference genome ARS-UCD2.0
cow
genome
assembly
updated 5 days ago by
Michael
55k • written 6 days ago by
am29
▴ 50
0
votes
1
reply
281
views
RNA-seq WGCNA anlysis
Rna-seq
WGCNA
updated 5 days ago by
ATpoint
86k • written 5 days ago by
SeoG
• 0
0
votes
0
replies
244
views
Splitting single cell data
ScRNA
5 days ago by
otieno43
▴ 40
0
votes
0
replies
260
views
News:
Online course - Flow cytometry data analysis with R/Bioconductor
R
Bioconductor
Flow-Cytometry
Cancer-Genomics
6 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
278
views
Help selecting WGCNA soft thresholding power
POWER
WGCNA
SOFT
updated 6 days ago by
andres.firrincieli
3.8k • written 6 days ago by
TNF_alpha
• 0
0
votes
0
replies
303
views
Deciding Between TOIL Processed Data (Xena) vs. TCGA Biolinks Data for DE Analysis
DESeq
TCGA
Xena
RNA-Seq
BIOLINKS
2 days ago by
lyan125
▴ 10
0
votes
1
reply
617
views
working with shapeit.
shapeit
updated 7 days ago by
sentigeo
• 0 • written 9 months ago by
sanchit000singhdr098
• 0
1
vote
1
reply
459
views
rRNA contamination in RNASeq fdata
contamination
rRNA
RNASeq
updated 7 days ago by
dsull
★ 7.1k • written 8 days ago by
rajdeepboral00
• 0
0
votes
2
replies
486
views
inserting Normalized count data
DESeq2
updated 7 days ago by
ATpoint
86k • written 8 days ago by
Saeed
▴ 10
2
votes
5
replies
705
views
high IgG background
background
IgG
signal
cuttag
updated 6 days ago by
ATpoint
86k • written 9 days ago by
17318598206
▴ 30
1
vote
3
replies
645
views
PRS calculation from two sample genotype results
prs
calculation
updated 6 days ago by
hakimbazol
▴ 50 • written 8 days ago by
Arun
• 0
0
votes
2
replies
426
views
Unexpected results: Conservation of cCREs
ccres
genes
encode
conservation
8 days ago by
Yacob
• 0
4
votes
3
replies
544
views
FastQC polyA and polyG trimming in RNA-seq
polyA
QC
trimming
RNA-seq
Fastq
6 days ago by
joonhong kwon
▴ 70
2
votes
4
replies
672
views
Finding Orthologs in Unannotated Genomes
orthologs
8 days ago by
triplee0305
▴ 10
1
vote
2
replies
555
views
Differential Expression for a predefined one or multiple genes and multiple testing
Deseq2
Multiple-testing
Differential-Expression
updated 8 days ago by
Gordon Smyth
★ 7.7k • written 12 days ago by
p-radwan.derbala
• 0
2
votes
0
replies
393
views
Herald:
The Biostar Herald for Monday, December 23, 2024
herald
8 days ago by
Biostar
3.3k
0
votes
6
replies
1.9k
views
dbSNP and indels
VCF
updated 8 days ago by
biology.may20
▴ 20 • written 2.0 years ago by
wonde2000
• 0
0
votes
1
reply
419
views
Retrieve query start and end positions on reverse strand with Pysam
python
alignment
Pysam
updated 7 days ago by
Mark
★ 1.6k • written 8 days ago by
María José
▴ 10
1
vote
0
replies
412
views
Job:
Looking for Internship/Junior Bioinformatics Opportunity
Opportunities
Bioinformatics
9 days ago by
Felix
▴ 10
119,957 results • Page
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Comment: is there any possible way I can tell whether the presence of more bands in the e
Comment: Create the correct contrast in limma when want to combine 2 or more groups
Trimming adapter sequences - is it necessary?
Comment: How to check for adapters?
Sequence Length Distribution From A Fastq File
Sjdboverhang Option In Star
Sjdboverhang Option In Star
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Answer: Compute P-Values for SNP Fst from Pairwise Fst Calculations (--weir-fst-pop)
by
Jorge Amigo
14k
Why exactly you want to have p-values, since Fst is already enough to describe differentiation degree? Have a look to [this paper][1], w…
Comment: FST Calculation: Resolving -nan Issue in Population Genetics Analysis
by
hashim.rana11
▴ 40
My research focuses on the Orthoptera species Schistocerca gregaria, which I collected from three locations: Kunming, Xi'an, and Yan'an. I …
Comment: Create the correct contrast in limma when want to combine 2 or more groups
by
Lila M
★ 1.3k
This is a great answer and exactly what I needed :) thank you very much
Comment: chip seq data visualization
by
nswati106
• 0
Thanks, i'll put screenshots soon of the plots you suggested. Do have a look if possible. but what do you mean by raw histone(deduplicated …
Comment: TCGA miRNA data query
by
jain72744
▴ 10
Trying to make a multi-omics-based deep learning model.
Comment: ORA with clusterProfiler
by
san96
▴ 140
Hello, in my case I used my count matrix (raw). Looks like: ``` > universe_arabidopsis <- read.delim("matriz_arabidopsis_2023.txt", heade…
Comment: How to check for adapters?
by
GenoMax
148k
Sequencing adapters would be significantly longer and more common (in terms of numbers) than UMI's.
Answer: Create the correct contrast in limma when want to combine 2 or more groups
by
Gordon Smyth
★ 7.7k
The general principle is that you should not give false information to limma. If you have determined that groups B and C are not genuinely …
Comment: Create the correct contrast in limma when want to combine 2 or more groups
by
Gordon Smyth
★ 7.7k
The two models aren't equivalent. The second model has one less model coefficient and one more residual degree of freedom. If there is DE b…
Comment: How to check for adapters?
by
sgupt46
• 0
Is there a way to know if the sequence is a sequencing adapter or UMI?
Answer: cant import VCF into OneMap, read.vcfR works but onemap_read_vcfR doesn't
by
Michael
55k
Also, I just saw a problem with your code, and this will very likely fix your problem. This should be: vcf_tfmpop <- onemap_read_…
Comment: cant import VCF into OneMap, read.vcfR works but onemap_read_vcfR doesn't
by
Michael
55k
OneMap used the [vcfR][1] package internally. Try the following: quit your R session and start R with --vanilla then update to the latest v…
Answer: cellxgene DNA Methylation data
by
LChart
4.7k
There are two issues here: (1) understanding the data and (2) understanding the data format. As regards (1): this is heavily processed D…
Comment: TCGA miRNA data query
by
GenoMax
148k
Should depend on your use case. What are you trying to do?
Answer: Create the correct contrast in limma when want to combine 2 or more groups
by
LChart
4.7k
For a simple linear model as above, the two specifications are not just "both correct:" they are equivalent and should produce the same res…
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