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1,009 results • Page
3 of 21
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0
votes
0
replies
129
views
barcode of TCR-sequencing
barcode
5 days ago by
yueli7
▴ 250
0
votes
0
replies
128
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 5 days ago by
Ram
43k • written 5 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
125
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 5 days ago by
Ram
43k • written 5 days ago by
Alexandros
• 0
0
votes
1
reply
170
views
unable to get feature count results
featureCounts
updated 4 days ago by
Ram
43k • written 5 days ago by
Ravita
• 0
0
votes
3
replies
280
views
KEGG Pathways
r
RNA-seq
updated 4 days ago by
Ram
43k • written 5 days ago by
Sudip
• 0
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 5 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
133
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
5 days ago by
Bine
▴ 60
0
votes
1
reply
284
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
5 days ago by
David Langenberger
11k
0
votes
1
reply
189
views
Deseq2
Deseq2
updated 5 days ago by
Jack Tierney
▴ 360 • written 5 days ago by
Sudip
• 0
1
vote
1
reply
229
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 5 days ago by
Michael
54k • written 5 days ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
278
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 5 days ago by
Lluís R.
★ 1.2k • written 5 days ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
198
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 5 days ago by
ATpoint
82k • written 5 days ago by
Sudip
• 0
1
vote
2
replies
226
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 4 days ago by
Ram
43k • written 5 days ago by
Ravita
• 0
0
votes
0
replies
113
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
5 days ago by
Adyasha
• 0
0
votes
0
replies
115
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
5 days ago by
fanglujing
▴ 60
0
votes
0
replies
133
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
5 days ago by
Jacob
• 0
0
votes
3
replies
743
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 5 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
272
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 5 days ago by
Ram
43k • written 5 days ago by
Hamtaro
▴ 50
0
votes
1
reply
182
views
Differential Accessibility
DiffBind
updated 5 days ago by
Ram
43k • written 5 days ago by
Shloka
• 0
0
votes
3
replies
287
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 5 days ago by
GenoMax
142k • written 5 days ago by
kim
• 0
3
votes
2
replies
378
views
Extract protein sequence
fasta
alignment
blast
4 days ago by
anna
▴ 20
3
votes
3
replies
324
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 5 days ago by
noodle
▴ 580 • written 6 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
168
views
metagenomic virome quality assessment
viromics
metagenomics
updated 5 days ago by
Ram
43k • written 6 days ago by
Petchimuthu
• 0
3
votes
7
replies
344
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
5 days ago by
salias
• 0
0
votes
0
replies
125
views
Using limma in methylation EM-seq?
EM-seq
methylation
5 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
589
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
5 days ago by
e.r.zakiev
▴ 210
0
votes
0
replies
124
views
Synteny analysis
bacterial
synteny
genome
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Namil
• 0
0
votes
4
replies
262
views
Genbank File Format
gbkformat
5 days ago by
alenew.am
• 0
0
votes
5
replies
422
views
How should I make kallisto indexes?
kallisto
updated 5 days ago by
dsull
★ 6.0k • written 20 days ago by
bioinfo
▴ 150
0
votes
0
replies
228
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
6 days ago by
SSSJec
• 0
0
votes
3
replies
217
views
Software to separate reads from different individuals
software
development
nanopore
updated 5 days ago by
GenoMax
142k • written 6 days ago by
njornet
▴ 20
0
votes
0
replies
93
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
6 days ago by
David
• 0
0
votes
2
replies
227
views
How to update R on ubuntu
installation
update
R
apt-get
6 days ago by
Bosberg
▴ 50
4
votes
0
replies
135
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
6 days ago by
Biostar
2.7k
1
vote
1
reply
144
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Ruqaiya
• 0
0
votes
1
reply
274
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 6 days ago by
trausch
★ 1.9k • written 22 days ago by
zec018
• 0
0
votes
0
replies
108
views
LEfSe
LEfSe
6 days ago by
benkosta
• 0
0
votes
0
replies
89
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
6 days ago by
Sara
▴ 30
1
vote
4
replies
396
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
6 days ago by
hagl
▴ 10
0
votes
5
replies
301
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 2 days ago by
Mohamed Abderrahmane
▴ 20 • written 6 days ago by
matteo.levorato
• 0
0
votes
2
replies
160
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
6 days ago by
Lluís R.
★ 1.2k
0
votes
1
reply
146
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 6 days ago by
i.sudbery
19k • written 6 days ago by
DOBI
• 0
0
votes
0
replies
100
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
6 days ago by
atharvakarkare14
▴ 30
7
votes
16
replies
735
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
6 days ago by
Ruqaiya
• 0
0
votes
2
replies
205
views
What should I consider as FASTA for dataset?
PDB
FASTA
5 days ago by
Nafi
• 0
38
votes
24
replies
1.9k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 5 days ago by
i.sudbery
19k • written 7 days ago by
noodle
▴ 580
0
votes
0
replies
510
views
Differential accessibility using DiffBinf
diffbind
6 days ago by
Shloka
• 0
0
votes
0
replies
97
views
vg call vs vg surject
vg
variation
graphs
updated 6 days ago by
GenoMax
142k • written 6 days ago by
aliraza3119
• 0
0
votes
1
reply
137
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Winter
• 0
2
votes
7
replies
1.3k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 6 days ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
1,009 results • Page
3 of 21
Recent Votes
Answer: LD-prune variants while maintaining a list of SNPs
Comment: TaxID mapping file
Answer: LD-prune variants while maintaining a list of SNPs
Comment: Downloading full alignments from Pfam
Answer: Segmentation error while using a tool
What is the best way to rank genes for GSEA?
What is the best way to rank genes for GSEA?
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carlopecoraro2
★ 2.5k
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Recent Replies
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
▴ 30
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
▴ 30
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…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
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