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116,777 results • Page
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Herald:
The Biostar Herald for Monday, May 06, 2024
herald
just now by
Biostar
2.7k
0
votes
0
replies
17
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
1 hour ago by
Antonio
• 0
0
votes
0
replies
15
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 1 hour ago by
Ram
43k • written 1 hour ago by
sidrah.maryam
▴ 50
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
14
views
Normalizing AMR gene count data
abundance
RGI
updated 1 hour ago by
Ram
43k • written 1 hour ago by
arshad1292
▴ 100
0
votes
1
reply
53
views
error in R code
R
updated 1 hour ago by
Ram
43k • written 2 hours ago by
snajafy
• 0
0
votes
0
replies
35
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 1 hour ago by
Ram
43k • written 3 hours ago by
MICOS
• 0
0
votes
0
replies
36
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 4 hours ago by
Pierre Lindenbaum
161k • written 4 hours ago by
sarumonsus
• 0
0
votes
2
replies
181
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
10 minutes ago by
M.
▴ 30
0
votes
0
replies
56
views
How to implement an IGV to streamlit app?
python
streamlit
igv
5 hours ago by
avigail.shnaider
• 0
1
vote
5
replies
167
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 1 hour ago by
Ram
43k • written 7 hours ago by
snajafy
• 0
0
votes
2
replies
145
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 1 hour ago by
GenoMax
142k • written 18 hours ago by
mropri
▴ 150
0
votes
1
reply
251
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 13 hours ago by
aaron.stevens
• 0 • written 12 weeks ago by
sativus
▴ 20
2
votes
2
replies
169
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB
protein
STRING-DB-API
15 hours ago by
brandon
• 0
0
votes
0
replies
81
views
Gene ontology and homologs
gene-ontology
updated 1 hour ago by
Ram
43k • written 19 hours ago by
beshka194
• 0
0
votes
0
replies
72
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
20 hours ago by
KHURRAM SHAHZAD
• 0
1
vote
5
replies
257
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 10 minutes ago by
Ram
43k • written 23 hours ago by
snajafy
• 0
0
votes
0
replies
74
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
21 hours ago by
Christopher
• 0
4
votes
1
reply
181
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 5 hours ago by
zx8754
11k • written 1 day ago by
Jautis
▴ 560
2
votes
2
replies
260
views
Association study using SNP data
Association
Allele
Parentage
SNP
23 hours ago by
drajangirija
• 0
0
votes
0
replies
67
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
81
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
1 day ago by
DGTool
• 0
0
votes
0
replies
81
views
Seurat V5 integration
Seurat
samples
integration
combine
1 day ago by
starswillfade
▴ 10
0
votes
0
replies
92
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
1 day ago by
Yoosef
▴ 60
0
votes
1
reply
305
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 1 day ago by
GenoMax
142k • written 1 day ago by
tulip
• 0
3
votes
4
replies
324
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
just now by
SHN
▴ 40
4
votes
2
replies
207
views
GRCh38.gmap file
gnomix
gmap
1 day ago by
lorena9132
▴ 10
2
votes
3
replies
779
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 1 day ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
1
reply
216
views
creating batch colum for batch correction
batch-correction
combat
3 hours ago by
Expert
▴ 10
1
vote
4
replies
301
views
Segmentation error while using a tool
smalt
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
Ruqaiya
• 0
0
votes
1
reply
168
views
Help with DGEList function
DGEList
R
updated 16 hours ago by
marco.barr
▴ 90 • written 2 days ago by
Natali
• 0
0
votes
0
replies
112
views
Homer motif analysis
Homer
2 days ago by
daffodil
▴ 10
0
votes
1
reply
155
views
HCL database download
database
HCL
human
updated 2 days ago by
GenoMax
142k • written 2 days ago by
sooni
▴ 20
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
1 day ago by
Zhenyu Zhang
★ 1.2k
2
votes
1
reply
264
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 2 days ago by
chrchang523
10k • written 6 days ago by
8armed
▴ 10
0
votes
5
replies
313
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 2 days ago by
chrchang523
10k • written 2 days ago by
curious
▴ 750
0
votes
1
reply
170
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 7 hours ago by
andres.firrincieli
3.6k • written 2 days ago by
deepak180001
• 0
0
votes
1
reply
186
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 1 day ago by
Ram
43k • written 2 days ago by
Rob
▴ 170
0
votes
1
reply
182
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Ximena
• 0
0
votes
1
reply
176
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 2 days ago by
Ram
43k • written 2 days ago by
Valentina
• 0
0
votes
6
replies
384
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 2 days ago by
swbarnes2
14k • written 3 days ago by
Erina
• 0
0
votes
1
reply
171
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
updated 2 days ago by
swbarnes2
14k • written 2 days ago by
kalavattam
▴ 190
1
vote
3
replies
255
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
20 hours ago by
Lada
▴ 30
1
vote
0
replies
134
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 5 hours ago by
zx8754
11k • written 2 days ago by
Emilie
▴ 10
0
votes
0
replies
130
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
2 days ago by
Javier
• 0
0
votes
1
reply
221
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 2 days ago by
Thanujay S
• 0 • written 2 days ago by
yahn
• 0
0
votes
0
replies
127
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
2 days ago by
mikemakaveli1
• 0
2
votes
2
replies
207
views
Raw counts using stringtie
stringtie
RNA-seq
updated 2 days ago by
GenoMax
142k • written 2 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
125
views
Modify plot R mtDNA indel
plot
mtDNA
R
2 days ago by
marco.barr
▴ 90
0
votes
0
replies
242
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
3 days ago by
NorbertK
• 0
116,777 results • Page
1 of 2336
Recent Votes
Comment: Design matrix Differential expression analysis
UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
Comment: install.packages("imudata")
Answer: Can I merge Hi-C fastq files from different lanes?
Answer: Interpretation of output from MiXCR TCR sequencing
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
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Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Got it, thank you for your response. SN
Comment: How to interpret DEXseq results in therms of significance
by
Sara
▴ 30
Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
Comment: Tissue-specific DEG analysis with DEseq2
by
M.
▴ 30
Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Ram
43k
Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
Comment: Gene Specific coverage from WGS data
by
GenoMax
142k
This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
Ram
43k
Read the answers in the post, understand them and try to implement them.
Comment: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 10
Just using the normalized expression of Malat1 works.
Comment: Can I merge Hi-C fastq files from different lanes?
by
Winter
• 0
Awesome, thank you for the concise and straight-forward answer!
Comment: error in R code
by
ATpoint
82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
Comment: Gene Specific coverage from WGS data
by
1769mkc
★ 1.2k
"Also if is there any other quick way to find gene specific coverage" can you give some example so that its bit more clear what do you mean…
Answer: Tissue-specific DEG analysis with DEseq2
by
ATpoint
82k
I assume that all data are from the same experiment, without batch effects and can thus be quantitiatively compared: Many ways to do thi…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
snajafy
• 0
I am facing the same problem and I don't know how to solve the problem,....
Comment: install.packages("imudata")
by
zx8754
11k
[How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?](https://stackoverflow.com/q/25721884/680068)
Answer: install.packages("imudata")
by
ATpoint
82k
Welcome to this community. Please learn the most important lesson right away which is reading answers and learning from it. Users gave you …
Comment: install.packages("imudata")
by
marco.barr
▴ 90
You can install from github directly. Many R packages are not present in the CRAN repository or in Bioconductor( from Biocmanager). Also re…
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