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116,765 results • Page
1 of 2336
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1
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45
views
install package
package
install
updated 1 hour ago by
Mathew
▴ 40 • written 2 hours ago by
snajafy
• 0
0
votes
0
replies
15
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
50 minutes ago by
Christopher
• 0
2
votes
1
reply
103
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
filtering
independent
linkage
2 hours ago by
Jautis
▴ 540
0
votes
2
replies
169
views
Association study using SNP data
Association
Allele
Parentage
SNP
2 hours ago by
drajangirija
• 0
0
votes
0
replies
32
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
4 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
42
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
4 hours ago by
DGTool
• 0
0
votes
0
replies
39
views
Seurat V5 integration
Seurat
samples
integration
combine
6 hours ago by
starswillfade
▴ 10
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
53
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
10 hours ago by
Yoosef
▴ 60
0
votes
1
reply
146
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 3 hours ago by
GenoMax
142k • written 12 hours ago by
tulip
• 0
2
votes
3
replies
277
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 15 hours ago by
Gordon Smyth
★ 7.1k • written 1 day ago by
SHN
▴ 40
4
votes
2
replies
172
views
GRCh38.gmap file
gnomix
gmap
18 hours ago by
lorena9132
▴ 10
2
votes
3
replies
748
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
2
replies
181
views
creating batch colum for batch correction
batch-correction
combat
updated 22 hours ago by
Ram
43k • written 1 day ago by
Expert
▴ 10
1
vote
4
replies
258
views
Segmentation error while using a tool
smalt
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Ruqaiya
• 0
0
votes
0
replies
81
views
Help with DGEList function
DGEList
R
updated 21 hours ago by
Ram
43k • written 1 day ago by
Natali
• 0
0
votes
0
replies
82
views
Homer motif analysis
Homer
1 day ago by
daffodil
▴ 10
0
votes
1
reply
125
views
HCL database download
database
HCL
human
updated 1 day ago by
GenoMax
142k • written 1 day ago by
sooni
▴ 20
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
9 hours ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
232
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 1 day ago by
chrchang523
10k • written 5 days ago by
8armed
• 0
0
votes
5
replies
284
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 1 day ago by
chrchang523
10k • written 2 days ago by
curious
▴ 750
0
votes
0
replies
107
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 1 day ago by
Ram
43k • written 1 day ago by
deepak180001
• 0
0
votes
1
reply
154
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 21 hours ago by
Ram
43k • written 1 day ago by
Rob
▴ 170
0
votes
1
reply
149
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Ximena
• 0
0
votes
1
reply
146
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 1 day ago by
Ram
43k • written 1 day ago by
Valentina
• 0
0
votes
6
replies
347
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
Erina
• 0
0
votes
1
reply
143
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 1 day ago by
swbarnes2
14k • written 1 day ago by
kalavattam
▴ 190
1
vote
2
replies
149
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
1 hour ago by
Lada
▴ 30
0
votes
0
replies
106
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
1 day ago by
Emilie
• 0
0
votes
0
replies
104
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
2 days ago by
Javier
• 0
0
votes
1
reply
193
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 1 day ago by
Thanujay S
• 0 • written 2 days ago by
yahn
• 0
0
votes
0
replies
100
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
0
votes
0
replies
107
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 2 days ago by
Ram
43k • written 2 days ago by
M.
▴ 30
2
votes
2
replies
179
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
99
views
Modify plot R mtDNA indel
plot
mtDNA
R
2 days ago by
marco.barr
▴ 90
0
votes
0
replies
204
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
2 days ago by
NorbertK
• 0
2
votes
2
replies
185
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 21 hours ago by
Ram
43k • written 2 days ago by
carolofharvest
▴ 30
9
votes
9
replies
525
views
High Malat-1 expression in single cell data
single-cell
updated 21 hours ago by
Ram
43k • written 6 days ago by
carolofharvest
▴ 30
0
votes
2
replies
203
views
Downloading older version of a tool
Alignment
tools
1 day ago by
Ruqaiya
• 0
0
votes
0
replies
117
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
2 days ago by
rustykb
▴ 20
1
vote
1
reply
146
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 21 hours ago by
Ram
43k • written 2 days ago by
adi.gershon1
• 0
3
votes
5
replies
237
views
Generating mpileup file using samtools
mpileup
samtools
updated 2 days ago by
Joe
21k • written 2 days ago by
Ruqaiya
• 0
0
votes
5
replies
310
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 2 days ago by
b.contreras.moreira
▴ 180 • written 3 days ago by
JH
• 0
1
vote
3
replies
254
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Qi
• 0
0
votes
0
replies
114
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
2 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
257
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 2 days ago by
dthorbur
★ 1.9k • written 2 days ago by
Vijith
▴ 30
0
votes
0
replies
134
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
2 days ago by
Jeyong
• 0
0
votes
2
replies
718
views
homer not configured properly
Homer
makeTagDirectory
updated 2 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
242
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 2 days ago by
Alex Reynolds
35k • written 2 days ago by
SJP
• 0
0
votes
0
replies
128
views
Empty table plot using plotGseaTable()
FGSEA
1 day ago by
Chris
▴ 260
116,765 results • Page
1 of 2336
Recent Votes
Comment: agilent human all exon sureselct v7 bed file
Answer: install package
Comment: Overlap File for RACON Genome Polisher
Overlap File for RACON Genome Polisher
Answer: LD-prune variants while maintaining a list of SNPs
Comment: TaxID mapping file
Answer: LD-prune variants while maintaining a list of SNPs
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Recent Replies
Comment: agilent human all exon sureselct v7 bed file
by
MiladAD
▴ 10
God bless you man.
Answer: install package
by
Mathew
▴ 40
Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file
by
Lada
▴ 30
thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs
by
Jautis
▴ 540
I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data
by
drajangirija
• 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam
by
bef1
• 0
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
Comment: Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Expe
by
Mensur Dlakic
★ 27k
Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
Comment: The GDC Legacy Archive is retiring soon.
by
Zhenyu Zhang
★ 1.2k
If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Zhenyu Zhang
★ 1.2k
These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 40
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 40
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
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