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1,000 results • Page
3 of 20
Sort: Rank
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Votes
Replies
1
vote
4
replies
330
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
Joe
21k • written 11 days ago by
cput
• 0
0
votes
0
replies
127
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
11 days ago by
asalimih
▴ 60
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 11 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
0
votes
0
replies
115
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 11 days ago by
Ram
43k • written 11 days ago by
mathavanbioinfo
▴ 90
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 11 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
5
votes
7
replies
519
views
RNA seq analysis
DESeq
RNA-seq
4 days ago by
Jacek
▴ 20
0
votes
0
replies
152
views
Chance for trained without experience
bio
updated 11 days ago by
ATpoint
82k • written 11 days ago by
shehab
• 0
0
votes
0
replies
133
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
11 days ago by
Omics data mining
▴ 260
0
votes
2
replies
205
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
11 days ago by
njornet
▴ 20
0
votes
2
replies
235
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 11 days ago by
Adam
▴ 30 • written 11 days ago by
Darya
• 0
0
votes
5
replies
311
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 11 days ago by
Joe
21k • written 11 days ago by
Lemonhope
• 0
0
votes
0
replies
188
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
10 days ago by
Winter
• 0
0
votes
0
replies
112
views
meffil.snp.concordance
meffil
methylation
snp_concordance
12 days ago by
kyj222637
• 0
0
votes
1
reply
172
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 11 days ago by
Bastien Hervé
5.3k • written 12 days ago by
sooni
▴ 20
1
vote
3
replies
283
views
STAR aligner error
RNA-seq
STAR
slurm
updated 11 days ago by
Ram
43k • written 12 days ago by
M.
▴ 30
0
votes
0
replies
106
views
monocle 3-- Could not get node in small cluster
monocle3
12 days ago by
synat.keam
▴ 100
0
votes
2
replies
234
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
11 days ago by
Nicholas
• 0
0
votes
1
reply
277
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 12 days ago by
GenoMax
142k • written 12 days ago by
Sony
▴ 10
5
votes
5
replies
348
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
12 days ago by
Chris
▴ 280
0
votes
2
replies
249
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 11 days ago by
swbarnes2
14k • written 12 days ago by
ahmad.sajad4541
• 0
1
vote
9
replies
437
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 9 days ago by
i.sudbery
19k • written 12 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
188
views
student
epitranscriptomics
updated 12 days ago by
ATpoint
82k • written 12 days ago by
useriwa
• 0
0
votes
3
replies
215
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 12 days ago by
GenoMax
142k • written 12 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
324
views
Correlation Analysis
statistics
methylation
NGS
expression
8 days ago by
Researcher
▴ 30
1
vote
2
replies
210
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
12 days ago by
robert.flynn.21
• 0
0
votes
0
replies
131
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
13 days ago by
Scott McKay
▴ 30
0
votes
0
replies
117
views
Cellphonedb results
cpdb
visulization
cellphonedb
13 days ago by
piotto
▴ 20
0
votes
0
replies
130
views
Cox Model with interaction item interpretation
Cox
13 days ago by
Bine
▴ 60
0
votes
0
replies
117
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
10 days ago by
Javier
• 0
1
vote
7
replies
580
views
Question regarding WGCNA
WGCNA
Network-construction
10 days ago by
deepak
• 0
0
votes
0
replies
117
views
vdjtools
vdjtools
13 days ago by
yueli7
▴ 250
0
votes
1
reply
315
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 12 days ago by
andres.firrincieli
3.6k • written 13 days ago by
Antonio
• 0
0
votes
0
replies
132
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 13 days ago by
Ram
43k • written 13 days ago by
sidrah.maryam
▴ 50
0
votes
0
replies
113
views
Normalizing AMR gene count data
abundance
RGI
updated 13 days ago by
Ram
43k • written 13 days ago by
arshad1292
▴ 100
1
vote
1
reply
192
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 3 days ago by
Jordan M Eizenga
▴ 460 • written 13 days ago by
sarumonsus
▴ 10
0
votes
0
replies
135
views
How to implement an IGV to streamlit app?
python
streamlit
igv
13 days ago by
avigail.shnaider
• 0
0
votes
0
replies
140
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
14 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
132
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
14 days ago by
Christopher
• 0
0
votes
0
replies
133
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
14 days ago by
DGTool
▴ 20
2
votes
3
replies
355
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 10 days ago by
bk11
★ 2.5k • written 14 days ago by
Yoosef
▴ 60
0
votes
1
reply
286
views
creating batch colum for batch correction
batch-correction
combat
13 days ago by
Expert
▴ 10
0
votes
1
reply
250
views
Help with DGEList function
DGEList
R
updated 14 days ago by
marco.barr
▴ 130 • written 15 days ago by
Natali
• 0
0
votes
0
replies
173
views
Homer motif analysis
Homer
15 days ago by
daffodil
▴ 10
0
votes
2
replies
283
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 9 days ago by
GenoMax
142k • written 16 days ago by
Ximena
• 0
0
votes
1
reply
225
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 15 days ago by
Ram
43k • written 16 days ago by
Valentina
• 0
0
votes
6
replies
494
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 16 days ago by
swbarnes2
14k • written 16 days ago by
Erina
• 0
1
vote
3
replies
345
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
14 days ago by
Lada
▴ 30
1
vote
0
replies
162
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 13 days ago by
zx8754
11k • written 16 days ago by
Emilie
▴ 10
0
votes
0
replies
150
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
16 days ago by
Javier
• 0
0
votes
2
replies
312
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 7 days ago by
Zhenyu Zhang
★ 1.2k • written 16 days ago by
yahn
• 0
1,000 results • Page
3 of 20
Recent Votes
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
C: Snakemake vs. Nextflow: strengths and weaknesses
Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
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Recent Awards •
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Scholar
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Pierre Lindenbaum
161k
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▴ 30
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synat.keam
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed
by
m13113153781
• 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
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