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13,168 results • Page
3 of 264
Sort: Rank
Rank
Views
Votes
Replies
0
votes
3
replies
227
views
STAR aligner error
RNA-seq
STAR
slurm
updated 4 days ago by
Ram
43k • written 5 days ago by
M.
▴ 30
0
votes
0
replies
96
views
monocle 3-- Could not get node in small cluster
monocle3
5 days ago by
synat.keam
▴ 100
0
votes
2
replies
195
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
4 days ago by
Nicholas
• 0
1
vote
4
replies
365
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
5 days ago by
heelpPlease
• 0
0
votes
7
replies
476
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 4 days ago by
Wayne
★ 2.0k • written 6 days ago by
JACKY
▴ 140
0
votes
0
replies
111
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
464
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 5 days ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
0
votes
1
reply
244
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Sony
▴ 10
5
votes
5
replies
281
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
4 days ago by
Chris
▴ 280
0
votes
2
replies
211
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
ahmad.sajad4541
• 0
1
vote
9
replies
348
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 2 days ago by
i.sudbery
19k • written 5 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
163
views
student
epitranscriptomics
updated 5 days ago by
ATpoint
82k • written 5 days ago by
useriwa
• 0
0
votes
0
replies
108
views
Imputation of missing genotypes
panel
beagle
imputation
5 days ago by
analyst
▴ 50
0
votes
3
replies
170
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Assa Yeroslaviz
★ 1.8k
7
votes
1
reply
166
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 5 days ago by
dariober
14k • written 5 days ago by
nhaus
▴ 360
2
votes
2
replies
172
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
4 days ago by
Zeng Jingyu
▴ 60
1
vote
2
replies
259
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 5 days ago by
Weiwen
• 0 • written 6 days ago by
MICOS
▴ 10
0
votes
4
replies
268
views
Correlation Analysis
statistics
methylation
NGS
expression
1 day ago by
Researcher
▴ 30
1
vote
2
replies
175
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
5 days ago by
robert.flynn.21
• 0
1
vote
1
reply
215
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 5 days ago by
Michael
54k • written 6 days ago by
Guillermo
• 0
1
vote
5
replies
338
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 4 days ago by
Michael
54k • written 5 days ago by
qwertyuiop26
• 0
0
votes
1
reply
174
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 5 days ago by
ATpoint
82k • written 6 days ago by
MAPK2
▴ 40
0
votes
2
replies
250
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 5 days ago by
Xiaofen
• 0 • written 5 days ago by
toddknutson
▴ 60
0
votes
1
reply
132
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 5 days ago by
LChart
3.9k • written 5 days ago by
David
• 0
2
votes
2
replies
177
views
Where to get the following bed file?
WES
bed
reference
file
updated 6 days ago by
GenoMax
142k • written 6 days ago by
wyuan37
• 0
0
votes
0
replies
112
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
6 days ago by
Scott McKay
▴ 30
0
votes
0
replies
104
views
Cellphonedb results
cpdb
visulization
cellphonedb
6 days ago by
piotto
▴ 20
0
votes
0
replies
136
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
6 days ago by
belloy
• 0
1
vote
3
replies
246
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
Ngrin
• 0
1
vote
6
replies
695
views
anRichment is missing
WGCNA
anRichment
updated 6 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
1
vote
1
reply
206
views
Gene ontology and homologs
gene-ontology
updated 6 days ago by
geneontologyhelp
▴ 400 • written 7 days ago by
beshka194
• 0
1
vote
2
replies
236
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 6 days ago by
zx8754
11k • written 6 days ago by
snajafy
• 0
0
votes
0
replies
114
views
Cox Model with interaction item interpretation
Cox
6 days ago by
Bine
▴ 60
0
votes
0
replies
100
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
3 days ago by
Javier
• 0
1
vote
7
replies
495
views
Question regarding WGCNA
WGCNA
Network-construction
3 days ago by
deepak
• 0
0
votes
0
replies
105
views
vdjtools
vdjtools
6 days ago by
yueli7
▴ 250
1
vote
0
replies
148
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
6 days ago by
Biostar
2.7k
0
votes
1
reply
287
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 5 days ago by
andres.firrincieli
3.6k • written 6 days ago by
Antonio
• 0
0
votes
0
replies
116
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 6 days ago by
Ram
43k • written 6 days ago by
sidrah.maryam
▴ 50
0
votes
0
replies
101
views
Normalizing AMR gene count data
abundance
RGI
updated 6 days ago by
Ram
43k • written 6 days ago by
arshad1292
▴ 100
1
vote
0
replies
130
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
sarumonsus
▴ 10
0
votes
0
replies
120
views
How to implement an IGV to streamlit app?
python
streamlit
igv
6 days ago by
avigail.shnaider
• 0
1
vote
5
replies
325
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 6 days ago by
Ram
43k • written 6 days ago by
snajafy
• 0
0
votes
2
replies
272
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 6 days ago by
GenoMax
142k • written 7 days ago by
mropri
▴ 150
0
votes
1
reply
301
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 6 days ago by
aaron.stevens
• 0 • written 3 months ago by
sativus
▴ 20
2
votes
2
replies
240
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
7 days ago by
brandon
• 0
0
votes
0
replies
131
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
7 days ago by
KHURRAM SHAHZAD
• 0
3
votes
6
replies
432
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 4 hours ago by
Pine
▴ 20 • written 7 days ago by
snajafy
• 0
0
votes
0
replies
120
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
7 days ago by
Christopher
• 0
4
votes
1
reply
244
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 6 days ago by
zx8754
11k • written 8 days ago by
Jautis
▴ 560
13,168 results • Page
3 of 264
Recent Votes
C: Convert .Txt File To Bed File
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
Answer: install package
Answer: How I do lift over a Plink bim file from Hg18 to Hg19.
Answer: joint callset and vcf sorting, unknown TAG issue
Answer: joint callset and vcf sorting, unknown TAG issue
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Recent Awards •
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Popular Question
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rj.rezwan
• 0
Scholar
to
colindaven
6.4k
Scholar
to
pjb39
▴ 200
Popular Question
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Jen
▴ 70
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Pierre Lindenbaum
161k
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54k
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Kai_Qi
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Recent Replies
Answer: Nomalization - TCGA, RNA-seq and Microarray
by
Zhenyu Zhang
★ 1.2k
You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
by
ATpoint
82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Pine
▴ 20
This seems to indicate that the R verison you are using (or packages it depends on) are not compatible with the R version you are using any…
Answer: Tissue-specific DEG analysis with DEseq2
by
arctic
▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty
by
Mathew
▴ 100
Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Comment: Tissue-specific DEG analysis with DEseq2
by
BioinfGuru
★ 1.7k
I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> set the Number= to 0 instead of 1; I'm not sure it's a problem. > probably I should also change the Type to Flag ah yes, my bad ! (f…
Comment: Output file of satools flagstat empty
by
GenoMax
142k
If you posted the entire command line then you did not include `-O $MAPPING/${i}.mapping_stats.txt` in that.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum I see. I looked up and, although present, the TAG goes like this in both files: `##INFO=<ID=1000gALT,Number=0,Type=Flag,…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum much appreciated, thanks for the explanation and possible approaches to solve this. I'm not in the position to run `U…
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