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117,099 results • Page
1 of 2342
Sort: Rank
Rank
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Votes
Replies
1
vote
5
replies
142
views
Z score
Z
score
5 minutes ago by
Akash D
▴ 50
1
vote
4
replies
88
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
57 minutes ago by
NTerway
• 0
1
vote
2
replies
76
views
Unexpected read length from NGS
NGS
Illumina
updated 2 hours ago by
ATpoint
82k • written 4 hours ago by
QX
• 0
0
votes
0
replies
31
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
2 hours ago by
adarsh_pp
▴ 40
1
vote
6
replies
245
views
samtools write-index
samtools
updated 3 hours ago by
aw7
▴ 310 • written 1 day ago by
LucisTheFather
• 0
0
votes
2
replies
179
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 3 hours ago by
i.sudbery
19k • written 1 day ago by
Varsha
• 0
799
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
1
vote
2
replies
88
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 2 hours ago by
ATpoint
82k • written 4 hours ago by
egascon
• 0
0
votes
0
replies
35
views
GWAS or QTL mapping in RIL population
GWAS
RIL
4 hours ago by
韩雨
• 0
0
votes
0
replies
40
views
VEP annotation tool: "." isn't numeric in addition (+)
annotation
Variant
VEP
warning
VCF
4 hours ago by
emmanouil.a
▴ 120
11
votes
9
replies
6.5k
views
6 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 4 minutes ago by
i.sudbery
19k • written 2.4 years ago by
wmsalsah
▴ 10
0
votes
1
reply
220
views
GWAS Phenotypes
GWAS
updated 5 hours ago by
韩雨
• 0 • written 5 weeks ago by
solomoncharles77
▴ 90
5
votes
4
replies
5.1k
views
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 4 hours ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
0
votes
1
reply
62
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 2 hours ago by
GenoMax
142k • written 5 hours ago by
azeu
• 0
0
votes
0
replies
27
views
Assigning Micro-C read pairs to nucleosomes called from MNase-seq data?
Hi-C
MNase-Seq
6 hours ago by
Linus
• 0
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 6 hours ago by
Akash D
▴ 50 • written 6.5 years ago by
rob.costa1234
▴ 310
0
votes
1
reply
79
views
Free AI for R programming
Programming
R
updated 2 hours ago by
GenoMax
142k • written 6 hours ago by
mohamadzare6022
▴ 10
7
votes
13
replies
689
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 2 minutes ago by
i.sudbery
19k • written 29 days ago by
Estevão
▴ 10
0
votes
0
replies
64
views
Extracting haplotype-specific annotations from splicing graph
vg
10 hours ago by
Juhyun
• 0
0
votes
0
replies
57
views
miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
scRNA-seq
seurat
miloR
10 hours ago by
shuaizh117
▴ 10
1
vote
1
reply
113
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 12 hours ago by
Jeremy
▴ 910 • written 14 hours ago by
Mohamed Samir
▴ 30
0
votes
0
replies
61
views
Phyloseq returning black bars for plot_bar
phyloseq
bioconductor
R
14 hours ago by
Jacob
• 0
1
vote
8
replies
834
views
Random Access remote BAM files
htslib
BAM
updated 16 hours ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 10
0
votes
3
replies
153
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
updated 15 hours ago by
GenoMax
142k • written 16 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
70
views
Cancer vs Normal Cell Classification Based on SNVs
cancer
17 hours ago by
dglad
• 0
0
votes
4
replies
181
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
16 hours ago by
reza
▴ 300
0
votes
1
reply
95
views
Flag multiple filtering steps on VCF files using VEP
FILTERING
VEP
VCF
updated 17 hours ago by
Pierre Lindenbaum
162k • written 17 hours ago by
avelarbio46
▴ 30
0
votes
1
reply
110
views
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
RNAseq
updated 18 hours ago by
GenoMax
142k • written 18 hours ago by
Fossil
• 0
1
vote
1
reply
151
views
Construction of circos plot from WGS data
WGS
Circos
updated 18 hours ago by
Ram
44k • written 1 day ago by
Anitha
▴ 10
1
vote
3
replies
201
views
Trimmomatic running but files containing purged reads are empty
fastqc
fastq
trimmomatic
updated 20 hours ago by
GenoMax
142k • written 20 hours ago by
Wilber0x
▴ 50
0
votes
0
replies
75
views
How to find nucleotide changes and the predicted effect when comparing two genomes
BLAST
alignment
updated 18 hours ago by
Ram
44k • written 21 hours ago by
Melissa
• 0
5
votes
3
replies
170
views
FastQC interpretation - 16S sequencing
interpretation
amplicon
Fastqc
16S
updated 22 hours ago by
GenoMax
142k • written 22 hours ago by
Christopher
▴ 10
0
votes
0
replies
82
views
Subset of ATAC-seq peaks has high variance
atac-seq
edgeR
R
normalization
8 hours ago by
Tim
• 0
2
votes
6
replies
258
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
7 hours ago by
anikcropscience
▴ 230
0
votes
0
replies
85
views
KEGG pathway enrichment analysis in Zea mays with R
KEGG
Zea-mays
R
updated 18 hours ago by
Ram
44k • written 23 hours ago by
letizia.ottaviani
• 0
0
votes
6
replies
247
views
from CRAM to fastq
FASTQ
WGS
CRAM
updated 16 hours ago by
ATpoint
82k • written 1 day ago by
machaalani29
• 0
0
votes
0
replies
86
views
News:
Bioinformatic Analysis of Transposable Elements course
Genome-Annotation
TE
Manual-Curation
Transposable-Elements
updated 18 hours ago by
Ram
44k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
113
views
No output when converting transcript IDs to gene symbols
RNA-seq
updated 18 hours ago by
Ram
44k • written 1 day ago by
ashkan
▴ 160
3
votes
1
reply
145
views
vg autoindex seems stuck after a week of running
vg
pangenome
updated 1 day ago by
Jouni Sirén
▴ 380 • written 1 day ago by
StevieP
▴ 10
0
votes
0
replies
97
views
MAFFT alignment report
RNA
Alignment
MAFFT
Linux
updated 18 hours ago by
Ram
44k • written 1 day ago by
Ghada
• 0
0
votes
3
replies
280
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 1 day ago by
colindaven
6.4k • written 2 days ago by
Bjorn
• 0
0
votes
1
reply
141
views
How to get 2 seurat objects into a DEseq
Seurat
DEseq
updated 18 hours ago by
Ram
44k • written 1 day ago by
He11oJe11o
• 0
0
votes
0
replies
86
views
Rescaling normalized enrichment score (NES)
heatmap
1 day ago by
CTLong
▴ 110
0
votes
2
replies
159
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
1 day ago by
kmat
• 0
0
votes
1
reply
141
views
Mapping difference with BWA
variant-calling
samtools
bam
BWA
genomics
updated 1 day ago by
ATpoint
82k • written 1 day ago by
rj.rezwan
• 0
0
votes
0
replies
97
views
Kegg Pathways to Circos
Genomics
KEGG
Circos
1 day ago by
dlera.lozano
▴ 10
0
votes
0
replies
108
views
DIFFBIND boxplot results, p value not significant
DiffBind
ChIP-seq
22 hours ago by
RD
▴ 10
3
votes
6
replies
324
views
Problem in getting geo file through GEOQUERY
geoquery
Geo
updated 18 hours ago by
Ram
44k • written 1 day ago by
anasjamshed
▴ 120
0
votes
1
reply
171
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
updated 1 day ago by
andersdetermig
▴ 20 • written 2 days ago by
Christopher
• 0
0
votes
2
replies
303
views
transanno liftvcf "Error: length of chromosome [chr] is not equal to length in chain file. Are you using correct reference?"
liftover
transanno
1 day ago by
ezz3
• 0
117,099 results • Page
1 of 2342
Recent Votes
Comment: log2 fold change in RNA-seq analysis
Comment: log2 fold change in RNA-seq analysis
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
correct way of analyzing cell proportions in singlecell data
Comment: How to interpret this plotMDS of three disease clusters?
gseGO: no term enriched under specific pvalueCutoff
Answer: Error with BiocParallel. No barcodes files found
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Recent Replies
Answer: Z score
by
Akash D
▴ 50
I made this. Z scored on log2FC? will anyone support me on this? 3 groups A,B,C
Comment: log2 fold change in RNA-seq analysis
by
i.sudbery
19k
There is no such thing as a fold change of -2. Fold change is expression_in_condition_A/expresssion_in_condition_B as expression is a…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
DE with 100s of samples (particulalry if your experiemental design is more complex than 2 condition DE) can stretch consumer grade hardware…
Comment: Error with BiocParallel. No barcodes files found
by
NTerway
• 0
Thank you for your help! I will try this out. I am trying to implement a collaborator's pipeline on my data and they only use SCE, scran an…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
ATpoint
82k
Once you have the counts any n is possible on a regular analysis-grade laptop or workstation. Even hundreds of samples. It's really the pre…
Comment: Error with BiocParallel. No barcodes files found
by
ATpoint
82k
You just tell the function to remove the prefix for you. Not on the actual file. Then you can add this information to the SCE, like `sce$da…
Comment: log2 fold change in RNA-seq analysis
by
May Ling
• 0
Thank you for your response. I apologize if my understanding is incomplete. I would like to ask: if I have a fold change of -2, how can I c…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
Yeah, a standard 3x3 bulk experiement is very analysable on pretty much most good consumer laptops these days.
Comment: Error with BiocParallel. No barcodes files found
by
NTerway
• 0
Thanks for the explanation! If I remove the prefix (GSM3972009_69_) then I will lose the sample annotation and cannot track them. I am more…
Comment: Unexpected read length from NGS
by
ATpoint
82k
Seconding this. Just ask them.
Answer: Error with BiocParallel. No barcodes files found
by
ATpoint
82k
The function assumes simply barcodes.tsv(.gz), genes.tsv(.gz) and matrix.mtx(.gz), without additional pre- or suffixes by default. You can …
Comment: Free AI for R programming
by
GenoMax
142k
Try: https://ai.tinybio.cloud/
Comment: How to interpret this plotMDS of three disease clusters?
by
ATpoint
82k
arrayWeights is imo always a good idea with human (or generally large) cohorts. What you can also do is to use something like sva to estima…
Comment: Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Po
by
GenoMax
142k
Not what you want to hear but it is possible that the Ab data is not good quality as the cellranger message says (assuming everything ran p…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
ATpoint
82k
Bulk RNA-seq is way less intensive in every regard than single-cell. Whatever you buy, be sure it's upgradable, meaning, no Mac :)
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